Query 036141
Match_columns 220
No_of_seqs 113 out of 1345
Neff 9.8
Searched_HMMs 46136
Date Fri Mar 29 09:51:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036141.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036141hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14223 UBN2: gag-polypeptide 99.8 1.9E-19 4E-24 126.3 11.8 110 20-141 1-116 (119)
2 PF14227 UBN2_2: gag-polypepti 99.8 1.6E-18 3.6E-23 121.5 12.2 111 19-141 1-114 (119)
3 PF14244 UBN2_3: gag-polypepti 99.4 1.7E-13 3.7E-18 100.0 6.0 75 1-75 63-140 (152)
4 PF00098 zf-CCHC: Zinc knuckle 98.8 3E-09 6.5E-14 48.1 1.7 17 190-206 2-18 (18)
5 PF03732 Retrotrans_gag: Retro 98.3 1.9E-06 4.1E-11 57.4 5.6 71 19-106 26-96 (96)
6 COG5082 AIR1 Arginine methyltr 98.2 8.1E-07 1.7E-11 65.5 2.6 40 168-207 58-117 (190)
7 PF13696 zf-CCHC_2: Zinc knuck 98.1 1.4E-06 3E-11 45.0 1.1 21 189-209 9-29 (32)
8 PTZ00368 universal minicircle 97.8 1.1E-05 2.3E-10 58.6 2.3 36 172-207 79-122 (148)
9 PTZ00368 universal minicircle 97.6 6.7E-05 1.5E-09 54.4 3.5 37 172-208 54-97 (148)
10 PF14787 zf-CCHC_5: GAG-polypr 97.4 9.7E-05 2.1E-09 38.9 1.5 25 190-214 4-28 (36)
11 KOG4400 E3 ubiquitin ligase in 97.3 0.00015 3.2E-09 57.7 2.8 41 171-211 144-187 (261)
12 smart00343 ZnF_C2HC zinc finge 97.3 0.00012 2.6E-09 36.4 1.0 18 190-207 1-18 (26)
13 PF13917 zf-CCHC_3: Zinc knuck 97.2 0.0002 4.4E-09 39.7 1.8 19 188-206 4-22 (42)
14 KOG0119 Splicing factor 1/bran 97.0 0.0022 4.8E-08 53.9 6.1 45 163-207 254-304 (554)
15 COG5082 AIR1 Arginine methyltr 96.8 0.00081 1.8E-08 49.8 2.1 37 171-207 98-139 (190)
16 PF03564 DUF1759: Protein of u 96.7 0.0093 2E-07 42.9 7.3 96 3-111 33-136 (145)
17 PF14392 zf-CCHC_4: Zinc knuck 96.6 0.00066 1.4E-08 39.3 0.5 17 190-206 33-49 (49)
18 PF15288 zf-CCHC_6: Zinc knuck 96.6 0.0023 5.1E-08 34.8 2.4 23 189-211 2-26 (40)
19 PF00098 zf-CCHC: Zinc knuckle 95.7 0.0092 2E-07 26.7 1.7 17 172-188 2-18 (18)
20 KOG0109 RNA-binding protein LA 95.6 0.0046 1E-07 48.7 1.0 20 189-208 161-180 (346)
21 KOG4400 E3 ubiquitin ligase in 95.0 0.019 4.1E-07 45.7 2.7 45 167-211 69-115 (261)
22 COG5222 Uncharacterized conser 94.9 0.013 2.8E-07 46.4 1.4 22 189-210 177-198 (427)
23 PF02023 SCAN: SCAN domain; I 90.6 3.6 7.7E-05 27.3 8.7 79 45-135 6-85 (95)
24 PF00607 Gag_p24: gag gene pro 84.8 5.3 0.00012 30.6 7.0 40 21-69 107-147 (206)
25 PF14893 PNMA: PNMA 83.8 17 0.00036 30.1 9.8 53 19-73 229-282 (331)
26 KOG0341 DEAD-box protein abstr 83.8 0.37 8.1E-06 40.2 0.3 23 189-211 571-593 (610)
27 KOG0314 Predicted E3 ubiquitin 83.6 0.75 1.6E-05 39.1 2.0 38 171-208 134-178 (448)
28 PF12353 eIF3g: Eukaryotic tra 83.1 0.64 1.4E-05 32.7 1.2 20 188-208 106-125 (128)
29 COG1198 PriA Primosomal protei 81.3 1.1 2.3E-05 41.0 2.2 40 170-210 435-484 (730)
30 KOG2044 5'-3' exonuclease HKE1 77.6 1.1 2.5E-05 40.6 1.2 20 190-209 262-281 (931)
31 KOG2560 RNA splicing factor - 72.5 0.67 1.5E-05 39.2 -1.4 27 187-213 111-137 (529)
32 KOG2673 Uncharacterized conser 72.3 2.1 4.5E-05 36.4 1.4 20 191-210 131-150 (485)
33 COG2879 Uncharacterized small 71.5 13 0.00028 22.5 4.2 31 99-130 17-50 (65)
34 PF07295 DUF1451: Protein of u 69.7 16 0.00034 26.4 5.2 30 168-197 110-139 (146)
35 KOG4602 Nanos and related prot 69.6 4.3 9.3E-05 31.8 2.5 46 164-209 227-292 (318)
36 KOG0107 Alternative splicing f 66.1 3.3 7.1E-05 30.7 1.2 16 191-206 103-118 (195)
37 PF09297 zf-NADH-PPase: NADH p 63.6 3 6.6E-05 21.4 0.4 26 171-196 4-29 (32)
38 PF13248 zf-ribbon_3: zinc-rib 63.4 4.9 0.00011 19.5 1.2 22 172-197 4-25 (26)
39 PF07754 DUF1610: Domain of un 62.5 5.8 0.00013 19.1 1.3 8 189-196 17-24 (24)
40 TIGR03859 PQQ_PqqD coenzyme PQ 61.7 32 0.0007 21.9 5.1 31 5-35 29-59 (81)
41 PF07904 Eaf7: Chromatin modif 61.6 7.6 0.00017 25.5 2.2 29 6-34 25-58 (91)
42 PRK00398 rpoP DNA-directed RNA 60.5 4.9 0.00011 22.5 1.0 26 172-197 5-30 (46)
43 PF07282 OrfB_Zn_ribbon: Putat 60.4 6.4 0.00014 24.1 1.6 29 171-199 29-57 (69)
44 PF13240 zinc_ribbon_2: zinc-r 60.1 6.4 0.00014 18.6 1.2 10 188-197 13-22 (23)
45 KOG3794 CBF1-interacting corep 58.6 4.2 9.2E-05 33.9 0.7 21 188-208 124-146 (453)
46 PRK14873 primosome assembly pr 57.3 7 0.00015 35.6 1.9 22 188-210 410-431 (665)
47 TIGR00595 priA primosomal prot 56.7 8.3 0.00018 33.9 2.2 22 188-209 240-261 (505)
48 PF15616 TerY-C: TerY-C metal 55.6 8.5 0.00018 27.2 1.7 34 169-202 76-119 (131)
49 PF05402 PqqD: Coenzyme PQQ sy 53.4 47 0.001 19.9 4.7 23 11-33 21-43 (68)
50 TIGR02642 phage_xxxx uncharact 53.2 8.5 0.00018 29.0 1.5 31 170-202 99-129 (186)
51 PF00684 DnaJ_CXXCXGXG: DnaJ c 52.9 16 0.00034 22.3 2.4 41 167-207 12-62 (66)
52 smart00647 IBR In Between Ring 52.2 11 0.00023 22.4 1.6 19 186-204 46-64 (64)
53 PRK11032 hypothetical protein; 52.1 63 0.0014 23.7 5.8 30 168-197 122-151 (160)
54 PRK05580 primosome assembly pr 51.5 11 0.00024 34.4 2.2 22 188-209 408-429 (679)
55 PRK11582 flagella biosynthesis 51.0 59 0.0013 23.7 5.3 21 53-73 102-122 (169)
56 TIGR03823 FliZ flagellar regul 50.2 56 0.0012 23.8 5.1 21 53-73 102-122 (168)
57 COG0484 DnaJ DnaJ-class molecu 49.5 17 0.00036 30.5 2.8 42 169-210 158-206 (371)
58 KOG3116 Predicted C3H1-type Zn 49.2 4.5 9.8E-05 28.9 -0.5 19 190-208 29-47 (177)
59 COG5179 TAF1 Transcription ini 49.2 8.1 0.00018 34.4 0.9 21 188-208 937-959 (968)
60 KOG3188 Uncharacterized conser 49.0 1.1E+02 0.0024 23.5 6.7 27 99-128 23-49 (246)
61 COG5222 Uncharacterized conser 47.3 31 0.00067 27.9 3.8 19 170-188 176-194 (427)
62 PHA02540 61 DNA primase; Provi 46.3 9.4 0.0002 31.6 0.9 31 170-200 27-67 (337)
63 PF03604 DNA_RNApol_7kD: DNA d 46.0 17 0.00037 18.8 1.5 23 173-196 3-25 (32)
64 KOG0109 RNA-binding protein LA 44.4 12 0.00025 30.2 1.1 21 169-189 159-179 (346)
65 PF05310 Tenui_NS3: Tenuivirus 43.4 7.8 0.00017 28.7 0.0 17 187-203 97-113 (186)
66 PRK04023 DNA polymerase II lar 43.3 19 0.00042 34.2 2.4 37 170-208 626-670 (1121)
67 PF14684 Tricorn_C1: Tricorn p 42.1 72 0.0016 19.6 4.2 52 22-73 8-61 (70)
68 COG2816 NPY1 NTP pyrophosphohy 40.2 16 0.00035 29.3 1.3 34 171-205 112-145 (279)
69 PHA00689 hypothetical protein 40.1 11 0.00024 21.4 0.3 11 189-199 18-28 (62)
70 COG1571 Predicted DNA-binding 39.3 18 0.0004 30.8 1.6 34 170-204 350-383 (421)
71 PF05741 zf-nanos: Nanos RNA b 39.0 13 0.00028 21.9 0.4 23 185-207 27-55 (55)
72 smart00400 ZnF_CHCC zinc finge 39.0 23 0.0005 20.5 1.6 11 190-200 25-35 (55)
73 TIGR02606 antidote_CC2985 puta 38.9 84 0.0018 19.3 4.1 36 102-137 4-39 (69)
74 PF13376 OmdA: Bacteriocin-pro 37.2 92 0.002 18.6 4.7 28 7-34 5-32 (63)
75 COG1644 RPB10 DNA-directed RNA 36.8 14 0.00031 22.2 0.4 8 190-197 6-13 (63)
76 PF09779 Ima1_N: Ima1 N-termin 36.5 32 0.00069 24.2 2.2 32 172-203 2-35 (131)
77 PF09889 DUF2116: Uncharacteri 36.4 18 0.0004 21.6 0.8 10 188-197 3-12 (59)
78 PF15629 Perm-CXXC: Permuted s 36.3 25 0.00055 18.1 1.2 12 185-196 13-24 (32)
79 PF01807 zf-CHC2: CHC2 zinc fi 36.2 14 0.0003 24.5 0.3 12 189-200 55-66 (97)
80 KOG0119 Splicing factor 1/bran 35.7 19 0.00042 31.2 1.1 20 189-208 262-281 (554)
81 PF06757 Ins_allergen_rp: Inse 35.5 1.8E+02 0.004 21.5 6.5 80 49-136 64-145 (179)
82 PF03693 RHH_2: Uncharacterise 35.4 1.2E+02 0.0026 19.3 4.7 32 102-133 7-38 (80)
83 PRK05772 translation initiatio 34.9 2.8E+02 0.006 23.4 10.4 64 16-79 40-105 (363)
84 COG5420 Uncharacterized conser 34.2 59 0.0013 19.7 2.7 14 100-113 32-45 (71)
85 COG3357 Predicted transcriptio 33.7 81 0.0017 20.7 3.5 25 110-134 7-31 (97)
86 PF06689 zf-C4_ClpX: ClpX C4-t 33.6 17 0.00036 19.9 0.3 11 189-199 2-12 (41)
87 KOG3497 DNA-directed RNA polym 33.3 16 0.00034 21.8 0.2 8 190-197 6-13 (69)
88 smart00659 RPOLCX RNA polymera 33.1 25 0.00054 19.6 1.0 25 172-197 4-28 (44)
89 KOG4451 Uncharacterized conser 33.0 57 0.0012 25.4 3.1 18 189-206 250-268 (286)
90 PF13821 DUF4187: Domain of un 32.7 20 0.00044 21.1 0.6 17 190-206 29-49 (55)
91 PF01194 RNA_pol_N: RNA polyme 32.7 20 0.00043 21.6 0.5 8 190-197 6-13 (60)
92 PF14353 CpXC: CpXC protein 32.6 21 0.00045 24.9 0.8 15 190-204 40-54 (128)
93 PF14567 SUKH_5: SMI1-KNR4 cel 32.2 97 0.0021 21.9 4.0 18 98-115 32-49 (132)
94 cd07936 SCAN SCAN oligomerizat 32.1 1.4E+02 0.0031 19.2 7.3 75 45-131 5-80 (85)
95 PF01475 FUR: Ferric uptake re 32.1 99 0.0021 21.0 4.1 32 16-47 20-51 (120)
96 KOG4204 Histone deacetylase co 31.7 1.3E+02 0.0029 23.5 5.1 53 17-70 125-177 (231)
97 PF10013 DUF2256: Uncharacteri 31.7 31 0.00067 19.0 1.2 12 186-197 6-17 (42)
98 COG1996 RPC10 DNA-directed RNA 31.6 24 0.00051 20.3 0.7 24 173-196 9-32 (49)
99 PF08792 A2L_zn_ribbon: A2L zi 31.5 28 0.0006 18.1 0.9 25 172-196 5-29 (33)
100 KOG2203 GTP-binding protein [G 31.3 1.3E+02 0.0027 27.1 5.3 52 21-72 479-532 (772)
101 PF13395 HNH_4: HNH endonuclea 31.1 22 0.00047 20.7 0.5 7 191-197 1-7 (54)
102 KOG1244 Predicted transcriptio 30.8 32 0.0007 27.4 1.6 31 170-200 224-258 (336)
103 PF12156 ATPase-cat_bd: Putati 30.7 22 0.00048 23.1 0.6 9 190-198 2-10 (88)
104 KOG2985 Uncharacterized conser 30.4 13 0.00029 29.1 -0.5 18 189-206 82-99 (306)
105 KOG2344 Exocyst component prot 30.3 1.8E+02 0.0038 26.6 6.3 100 8-118 313-413 (623)
106 PF01485 IBR: IBR domain; Int 30.2 23 0.0005 20.8 0.6 19 186-204 46-64 (64)
107 PF14319 Zn_Tnp_IS91: Transpos 30.1 29 0.00062 23.7 1.1 25 172-196 44-68 (111)
108 COG4416 Com Mu-like prophage p 29.9 15 0.00032 21.4 -0.3 12 197-208 20-31 (60)
109 PLN00032 DNA-directed RNA poly 29.8 23 0.0005 22.0 0.5 8 190-197 6-13 (71)
110 PRK04016 DNA-directed RNA poly 29.5 23 0.00051 21.4 0.5 8 190-197 6-13 (62)
111 PF05515 Viral_NABP: Viral nuc 29.1 90 0.0019 21.8 3.3 20 189-208 63-82 (124)
112 smart00431 SCAN leucine rich r 28.8 2E+02 0.0043 19.8 7.1 78 45-134 5-83 (113)
113 PF09580 Spore_YhcN_YlaJ: Spor 28.1 2.4E+02 0.0053 20.6 6.1 51 23-73 120-176 (177)
114 COG1940 NagC Transcriptional r 27.7 32 0.0007 27.9 1.2 31 172-204 158-188 (314)
115 COG1545 Predicted nucleic-acid 27.3 31 0.00066 24.7 0.9 23 172-198 31-53 (140)
116 smart00778 Prim_Zn_Ribbon Zinc 27.2 67 0.0015 17.2 2.0 26 171-196 4-33 (37)
117 PF11023 DUF2614: Protein of u 27.1 28 0.0006 23.8 0.6 31 170-202 69-99 (114)
118 PF03902 Gal4_dimer: Gal4-like 27.1 1.4E+02 0.0031 17.7 4.2 26 60-85 3-28 (57)
119 KOG0122 Translation initiation 26.6 29 0.00063 27.3 0.7 18 190-208 121-138 (270)
120 COG4830 RPS26B Ribosomal prote 26.5 42 0.00092 22.3 1.3 10 188-197 20-29 (108)
121 PF11248 DUF3046: Protein of u 26.4 61 0.0013 19.7 1.9 20 16-35 40-59 (63)
122 TIGR00984 3a0801s03tim44 mitoc 26.4 4.1E+02 0.0088 22.6 7.7 91 20-119 170-266 (378)
123 PF12417 DUF3669: Zinc finger 25.9 60 0.0013 20.2 1.9 20 17-36 38-57 (72)
124 PF06424 PRP1_N: PRP1 splicing 25.8 2.5E+02 0.0054 19.9 5.2 47 21-67 64-111 (133)
125 PF13512 TPR_18: Tetratricopep 25.4 2E+02 0.0043 20.7 4.7 51 18-68 25-76 (142)
126 PF09133 SANTA: SANTA (SANT As 25.3 74 0.0016 20.9 2.4 21 94-114 71-91 (93)
127 PRK12380 hydrogenase nickel in 25.0 44 0.00095 22.9 1.3 26 171-198 71-96 (113)
128 PF00649 Copper-fist: Copper f 24.7 36 0.00078 18.5 0.6 15 191-206 11-25 (40)
129 PF07851 TMPIT: TMPIT-like pro 24.5 3.3E+02 0.0072 22.7 6.4 66 24-90 4-72 (330)
130 PRK05667 dnaG DNA primase; Val 24.5 46 0.00099 29.9 1.6 30 172-201 38-70 (580)
131 PF01844 HNH: HNH endonuclease 24.4 29 0.00063 18.9 0.3 11 191-201 1-11 (47)
132 PF06874 FBPase_2: Firmicute f 24.3 5.6E+02 0.012 23.5 8.1 81 25-121 59-148 (640)
133 PRK14291 chaperone protein Dna 24.2 79 0.0017 26.7 2.9 39 171-209 174-216 (382)
134 PF07023 DUF1315: Protein of u 24.1 57 0.0012 21.5 1.6 19 99-117 3-22 (93)
135 PF02093 Gag_p30: Gag P30 core 23.7 60 0.0013 24.9 1.9 28 48-75 129-157 (211)
136 KOG0403 Neoplastic transformat 23.5 2.2E+02 0.0048 24.9 5.3 15 95-109 616-630 (645)
137 cd01093 CRIB_PAK_like PAK (p21 23.4 50 0.0011 18.5 1.1 14 101-114 24-37 (46)
138 PF12760 Zn_Tnp_IS1595: Transp 23.3 45 0.00097 18.6 0.9 26 171-196 19-45 (46)
139 TIGR00100 hypA hydrogenase nic 23.3 49 0.0011 22.7 1.3 27 171-199 71-97 (115)
140 PF05667 DUF812: Protein of un 23.2 1.6E+02 0.0035 26.7 4.7 99 19-117 463-572 (594)
141 COG0735 Fur Fe2+/Zn2+ uptake r 23.2 2.4E+02 0.0051 20.1 4.9 30 16-45 33-62 (145)
142 COG0542 clpA ATP-binding subun 23.2 4.3E+02 0.0093 25.0 7.4 104 22-133 304-412 (786)
143 PF10664 NdhM: Cyanobacterial 23.1 1.7E+02 0.0036 19.7 3.6 44 55-117 41-84 (108)
144 COG2995 PqiA Uncharacterized p 23.0 56 0.0012 27.7 1.7 35 165-202 215-249 (418)
145 PRK02935 hypothetical protein; 22.7 46 0.00099 22.5 1.0 30 171-202 71-100 (110)
146 smart00547 ZnF_RBZ Zinc finger 22.7 60 0.0013 15.3 1.2 10 188-197 16-25 (26)
147 PRK09335 30S ribosomal protein 22.6 69 0.0015 21.2 1.7 8 189-196 21-28 (95)
148 cd07153 Fur_like Ferric uptake 22.2 2.4E+02 0.0052 18.8 4.6 29 17-45 14-42 (116)
149 PRK08334 translation initiatio 22.1 4.8E+02 0.01 22.0 10.2 64 16-79 38-103 (356)
150 TIGR01623 put_zinc_LRP1 putati 21.8 43 0.00092 18.5 0.6 23 173-197 2-24 (43)
151 PF09180 ProRS-C_1: Prolyl-tRN 21.8 38 0.00083 20.8 0.5 13 187-199 47-59 (68)
152 cd07562 Peptidase_S41_TRI Tric 21.8 3E+02 0.0066 21.7 5.7 54 21-74 5-60 (266)
153 TIGR03655 anti_R_Lar restricti 21.6 95 0.0021 17.8 2.1 29 172-200 3-38 (53)
154 PTZ00172 40S ribosomal protein 21.6 72 0.0016 21.6 1.7 8 189-196 21-28 (108)
155 PLN00186 ribosomal protein S26 21.5 74 0.0016 21.6 1.8 8 189-196 21-28 (109)
156 COG3120 Uncharacterized protei 21.3 1.7E+02 0.0036 20.5 3.5 16 2-17 56-71 (149)
157 COG1151 6Fe-6S prismane cluste 21.1 2.3E+02 0.005 25.4 5.1 72 63-137 474-545 (576)
158 TIGR03044 PS_II_psb27 photosys 21.1 3.2E+02 0.0068 19.5 5.0 33 101-134 85-124 (135)
159 PF08203 RNA_polI_A14: Yeast R 21.0 56 0.0012 20.7 1.1 16 92-107 59-74 (76)
160 PF05879 RHD3: Root hair defec 20.9 2.3E+02 0.005 26.5 5.4 60 7-68 437-496 (742)
161 TIGR01391 dnaG DNA primase, ca 20.8 59 0.0013 27.8 1.5 29 172-200 36-67 (415)
162 PF08112 ATP-synt_E_2: ATP syn 20.7 1.9E+02 0.0041 16.8 3.4 13 100-112 27-39 (56)
163 cd07563 Peptidase_S41_IRBP Int 20.7 1.9E+02 0.0042 22.5 4.3 51 23-73 3-56 (250)
164 KOG2607 CDK5 activator-binding 20.1 2.6E+02 0.0057 24.1 5.0 80 22-115 91-195 (505)
No 1
>PF14223 UBN2: gag-polypeptide of LTR copia-type
Probab=99.82 E-value=1.9e-19 Score=126.28 Aligned_cols=110 Identities=25% Similarity=0.417 Sum_probs=99.2
Q ss_pred ccHHHHHHHHHHHhccCCh---hHHhHHHHHHHHHh-cCCccHHHHHHHHHHHHHHHhhcccccCCcccHHHHHHHHHHH
Q 036141 20 KTAKDMWEYLKKVYNQDNT---AKRSHLEYEIARYS-QGNLSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQS 95 (220)
Q Consensus 20 ~ta~~~w~~L~~~f~~~~~---~~~~~l~~~~~~~~-q~~~sv~~y~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~ 95 (220)
+||+++|+.|+..|.+.+. +++..|+.+|..++ ++++||.+|+.+|..|+++|..+ |.++++ ..
T Consensus 1 ~tA~e~W~~L~~~y~~~~~~~~~~~~~L~~~l~~~k~~~~~sv~~y~~~~~~i~~~L~~~-g~~i~d-----------~~ 68 (119)
T PF14223_consen 1 KTAKEAWDALKKRYEGQSKVKQARVQQLKSQLENLKMKDGESVDEYISRLKEIVDELRAI-GKPISD-----------ED 68 (119)
T ss_pred ChHHHHHHHHHHHHcCCchHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHhhhhhhhc-CCcccc-----------hh
Confidence 5899999999999999999 99999999999998 67999999999999999999966 776654 66
Q ss_pred HHHHHHhhccchHHHHHHhhcCCCCCC--CHHHHHHHHHHHHHHHHHH
Q 036141 96 KRDQFLMKLRPKYEAARSNLMNRDLSP--SLDVCFKELLREEQRLATQ 141 (220)
Q Consensus 96 ~~~~~l~gLp~~~~~~~~~l~~~~~~~--sl~e~~~~l~~~e~~~~~~ 141 (220)
.|..+|.|||++|+.++..+....+.. |+++++..|..+|.++...
T Consensus 69 ~v~~iL~~Lp~~y~~~~~~i~~~~~~~~~t~~el~~~L~~~E~~~~~~ 116 (119)
T PF14223_consen 69 LVSKILRSLPPSYDTFVTAIRNSKDLPKMTLEELISRLLAEEMRLKSK 116 (119)
T ss_pred HHHHHHhcCCchhHHHHHHHHhcCCCCcCCHHHHHHHHHHHHHHHHHc
Confidence 666699999999999999999987776 9999999999999988763
No 2
>PF14227 UBN2_2: gag-polypeptide of LTR copia-type
Probab=99.79 E-value=1.6e-18 Score=121.47 Aligned_cols=111 Identities=25% Similarity=0.357 Sum_probs=96.8
Q ss_pred cccHHHHHHHHHHHhccCChhHHhHHHHHHHHHh-cCCccHHHHHHHHHHHHHHHhhcccccCCcccHHHHHHHHHHHHH
Q 036141 19 HKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYS-QGNLSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKR 97 (220)
Q Consensus 19 ~~ta~~~w~~L~~~f~~~~~~~~~~l~~~~~~~~-q~~~sv~~y~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~ 97 (220)
++||+++|+.|+..|...+.+....+.++|...+ .++.+|.+|+.+|..++++|..+ |.+++++.++.+
T Consensus 1 ~~ta~~~W~~L~~~y~~~~~~~~~~l~~kl~~~k~~~~~~v~~hi~~~~~l~~~L~~~-g~~i~d~~~~~~--------- 70 (119)
T PF14227_consen 1 CKTAKEMWDKLKKKYEKKSFANKIYLLRKLYSLKMDEGGSVRDHINEFRSLVNQLKSL-GVPIDDEDKVII--------- 70 (119)
T ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhHhccchhHHHHHHHHHHHHHhhccc-cccchHHHHHHH---------
Confidence 5799999999999999999888888888877766 56889999999999999999966 887776555555
Q ss_pred HHHHhhccchHHHHHHhhcCCC--CCCCHHHHHHHHHHHHHHHHHH
Q 036141 98 DQFLMKLRPKYEAARSNLMNRD--LSPSLDVCFKELLREEQRLATQ 141 (220)
Q Consensus 98 ~~~l~gLp~~~~~~~~~l~~~~--~~~sl~e~~~~l~~~e~~~~~~ 141 (220)
+|.+||++|++++.++.... ..+++++++..|..+|.++...
T Consensus 71 --lL~sLP~sy~~~~~~l~~~~~~~~~tl~~v~~~L~~ee~~~~~~ 114 (119)
T PF14227_consen 71 --LLSSLPPSYDSFVTALLYSKPEDELTLEEVKSKLLQEEERRKKS 114 (119)
T ss_pred --HHHcCCHhHHHHHHHHHccCCCCCcCHHHHHHHHHHHHHHHHhc
Confidence 99999999999999987754 7899999999999999887754
No 3
>PF14244 UBN2_3: gag-polypeptide of LTR copia-type
Probab=99.44 E-value=1.7e-13 Score=100.02 Aligned_cols=75 Identities=27% Similarity=0.656 Sum_probs=70.8
Q ss_pred CccccccchHHHHhhccccccHHHHHHHHHHHhccCC-hhHHhHHHHHHHHHhcCCccHHHHHHHHHHHH--HHHhhc
Q 036141 1 MTWIMGSIDQSLILNLKLHKTAKDMWEYLKKVYNQDN-TAKRSHLEYEIARYSQGNLSIQNYFSGFQNLW--AEYVDM 75 (220)
Q Consensus 1 ~s~i~~sl~~~~~~~~~~~~ta~~~w~~L~~~f~~~~-~~~~~~l~~~~~~~~q~~~sv~~y~~~~~~l~--~~L~~~ 75 (220)
++||+++|+++|...|..++||+++|+.|+++|...+ .+++++|+.+|...+|++.||.+|+.+|+.|+ .+|..+
T Consensus 63 ~swl~~sis~~i~~~i~~~~tak~~W~~L~~~f~~~~~~~r~~~L~~~l~~~kq~~~sv~ey~~~lk~l~~~~el~~~ 140 (152)
T PF14244_consen 63 LSWLLNSISPDILSTIIFCETAKEIWDALKERFSQKSNASRVFQLRNELHSLKQGDKSVTEYFNKLKSLWQEDELDEY 140 (152)
T ss_pred HHHHHHhhcHHHHhhhHhhhhHHHHHHHHHHHhhcccHHHHHHHHHHHHHHHhhCCCcHHHHHHHHHHHhHHHHHhCc
Confidence 5799999999999999999999999999999999888 89999999999999999999999999999999 667654
No 4
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=98.79 E-value=3e-09 Score=48.11 Aligned_cols=17 Identities=47% Similarity=1.239 Sum_probs=16.0
Q ss_pred cccccCCCCcccCCCCC
Q 036141 190 FCNYCKKPGHIIKECPT 206 (220)
Q Consensus 190 ~C~~Cgk~GH~~~~C~~ 206 (220)
.||+||+.||++++||+
T Consensus 2 ~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCPK 18 (18)
T ss_dssp BCTTTSCSSSCGCTSSS
T ss_pred cCcCCCCcCcccccCcc
Confidence 69999999999999985
No 5
>PF03732 Retrotrans_gag: Retrotransposon gag protein ; InterPro: IPR005162 Transposable elements (TEs) promote various chromosomal rearrangements more efficiently, and often more specifically, than other cellular processes. Retrotransposons are structurally similar to retroviruses and are bounded by long terminal repeats. This entry represents eukaryotic Gag or capsid-related retrotranspon-related proteins. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.
Probab=98.29 E-value=1.9e-06 Score=57.37 Aligned_cols=71 Identities=21% Similarity=0.368 Sum_probs=54.7
Q ss_pred cccHHHHHHHHHHHhccCChhHHhHHHHHHHHHhcCCccHHHHHHHHHHHHHHHhhcccccCCcccHHHHHHHHHHHHHH
Q 036141 19 HKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQGNLSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRD 98 (220)
Q Consensus 19 ~~ta~~~w~~L~~~f~~~~~~~~~~l~~~~~~~~q~~~sv~~y~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~ 98 (220)
..|..++-..|.+.|.+.. ....++.+|..++|+++||.+|+.+|+.|+..+.. .. +++.++.
T Consensus 26 ~~~W~~~~~~~~~~f~~~~--~~~~~~~~l~~l~Q~~esv~~y~~rf~~l~~~~~~----~~-----------~e~~~v~ 88 (96)
T PF03732_consen 26 FITWEEFKDAFRKRFFPPD--RKEQARQELNSLRQGNESVREYVNRFRELARRAPP----PM-----------DEEMLVE 88 (96)
T ss_pred CCCHHHHHHHHHHHHhhhh--ccccchhhhhhhhccCCcHHHHHHHHHHHHHHCCC----Cc-----------CHHHHHH
Confidence 3466777777777776532 34567788999999999999999999999988862 11 5677788
Q ss_pred HHHhhccc
Q 036141 99 QFLMKLRP 106 (220)
Q Consensus 99 ~~l~gLp~ 106 (220)
.|+.||.|
T Consensus 89 ~f~~GL~~ 96 (96)
T PF03732_consen 89 RFIRGLRP 96 (96)
T ss_pred HHHHCCCC
Confidence 89999975
No 6
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=98.22 E-value=8.1e-07 Score=65.46 Aligned_cols=40 Identities=30% Similarity=0.875 Sum_probs=33.0
Q ss_pred CCCcccccCCCCCccccccc---------C----------ccccccCCCCcccCCC-CCC
Q 036141 168 MRQVQCFSCKEYRHIVVKCA---------K----------KFCNYCKKPGHIIKEC-PTR 207 (220)
Q Consensus 168 ~~~~~~~~~~~~g~~~~~~~---------~----------~~C~~Cgk~GH~~~~C-~~k 207 (220)
..+..|++|+..||.+++|+ . ++|++||..||++++| |.+
T Consensus 58 ~~~~~C~nCg~~GH~~~DCP~~iC~~C~~~~H~s~~C~~~~~C~~Cg~~GH~~~dC~P~~ 117 (190)
T COG5082 58 EENPVCFNCGQNGHLRRDCPHSICYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDCNPSK 117 (190)
T ss_pred ccccccchhcccCcccccCChhHhhhcCCCCcccccCCcccccccccccCccccccCccc
Confidence 34667999999999999888 1 2799999999999999 443
No 7
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=98.09 E-value=1.4e-06 Score=44.98 Aligned_cols=21 Identities=38% Similarity=0.956 Sum_probs=18.2
Q ss_pred ccccccCCCCcccCCCCCCCC
Q 036141 189 KFCNYCKKPGHIIKECPTRPQ 209 (220)
Q Consensus 189 ~~C~~Cgk~GH~~~~C~~k~~ 209 (220)
-.|+.|+++||+.++||...+
T Consensus 9 Y~C~~C~~~GH~i~dCP~~~P 29 (32)
T PF13696_consen 9 YVCHRCGQKGHWIQDCPTNKP 29 (32)
T ss_pred CEeecCCCCCccHhHCCCCCC
Confidence 379999999999999998443
No 8
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=97.83 E-value=1.1e-05 Score=58.61 Aligned_cols=36 Identities=33% Similarity=0.970 Sum_probs=21.9
Q ss_pred ccccCCCCCcccccccCc--------cccccCCCCcccCCCCCC
Q 036141 172 QCFSCKEYRHIVVKCAKK--------FCNYCKKPGHIIKECPTR 207 (220)
Q Consensus 172 ~~~~~~~~g~~~~~~~~~--------~C~~Cgk~GH~~~~C~~k 207 (220)
.|+.|+..||..+.|+.. .||.|+..||++++||..
T Consensus 79 ~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~gH~~~~C~~~ 122 (148)
T PTZ00368 79 SCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPNA 122 (148)
T ss_pred ccCcCCCCCcccccCCCcccccccchhhcccCcCCcchhcCCCc
Confidence 466666666666655432 466666666666666653
No 9
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=97.59 E-value=6.7e-05 Score=54.41 Aligned_cols=37 Identities=35% Similarity=0.987 Sum_probs=22.6
Q ss_pred ccccCCCCCcccccccCc-------cccccCCCCcccCCCCCCC
Q 036141 172 QCFSCKEYRHIVVKCAKK-------FCNYCKKPGHIIKECPTRP 208 (220)
Q Consensus 172 ~~~~~~~~g~~~~~~~~~-------~C~~Cgk~GH~~~~C~~k~ 208 (220)
.|+.|+..||....|+.. .|+.|++.||++++|+.+.
T Consensus 54 ~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~~GH~~~~C~~~~ 97 (148)
T PTZ00368 54 SCYNCGKTGHLSRECPEAPPGSGPRSCYNCGQTGHISRECPNRA 97 (148)
T ss_pred ccCCCCCcCcCcccCCCcccCCCCcccCcCCCCCcccccCCCcc
Confidence 466666666666555443 4666666666666666643
No 10
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=97.38 E-value=9.7e-05 Score=38.88 Aligned_cols=25 Identities=24% Similarity=0.457 Sum_probs=16.6
Q ss_pred cccccCCCCcccCCCCCCCCCCcCC
Q 036141 190 FCNYCKKPGHIIKECPTRPQNCQAS 214 (220)
Q Consensus 190 ~C~~Cgk~GH~~~~C~~k~~~~~~~ 214 (220)
.|+.|||-.|++.+|+.+.+..++.
T Consensus 4 ~CprC~kg~Hwa~~C~sk~d~~G~p 28 (36)
T PF14787_consen 4 LCPRCGKGFHWASECRSKTDVDGNP 28 (36)
T ss_dssp C-TTTSSSCS-TTT---TCCCCCEE
T ss_pred cCcccCCCcchhhhhhhhhcccCCC
Confidence 5999999999999999988766543
No 11
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=97.33 E-value=0.00015 Score=57.70 Aligned_cols=41 Identities=34% Similarity=0.801 Sum_probs=36.7
Q ss_pred cccccCCCCCccccccc---CccccccCCCCcccCCCCCCCCCC
Q 036141 171 VQCFSCKEYRHIVVKCA---KKFCNYCKKPGHIIKECPTRPQNC 211 (220)
Q Consensus 171 ~~~~~~~~~g~~~~~~~---~~~C~~Cgk~GH~~~~C~~k~~~~ 211 (220)
..|+.|++.||....|+ ...|+.|++.||..++||......
T Consensus 144 ~~Cy~Cg~~GH~s~~C~~~~~~~c~~c~~~~h~~~~C~~~~~~~ 187 (261)
T KOG4400|consen 144 AKCYSCGEQGHISDDCPENKGGTCFRCGKVGHGSRDCPSKQKSK 187 (261)
T ss_pred CccCCCCcCCcchhhCCCCCCCccccCCCcceecccCCcccccc
Confidence 45999999999999999 779999999999999999877553
No 12
>smart00343 ZnF_C2HC zinc finger.
Probab=97.26 E-value=0.00012 Score=36.40 Aligned_cols=18 Identities=44% Similarity=1.084 Sum_probs=16.0
Q ss_pred cccccCCCCcccCCCCCC
Q 036141 190 FCNYCKKPGHIIKECPTR 207 (220)
Q Consensus 190 ~C~~Cgk~GH~~~~C~~k 207 (220)
.|++||+.||++++||..
T Consensus 1 ~C~~CG~~GH~~~~C~~~ 18 (26)
T smart00343 1 KCYNCGKEGHIARDCPKX 18 (26)
T ss_pred CCccCCCCCcchhhCCcc
Confidence 499999999999999843
No 13
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=97.24 E-value=0.0002 Score=39.67 Aligned_cols=19 Identities=37% Similarity=0.885 Sum_probs=17.0
Q ss_pred CccccccCCCCcccCCCCC
Q 036141 188 KKFCNYCKKPGHIIKECPT 206 (220)
Q Consensus 188 ~~~C~~Cgk~GH~~~~C~~ 206 (220)
...|.+|++.||+..+|++
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 3469999999999999996
No 14
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=96.95 E-value=0.0022 Score=53.93 Aligned_cols=45 Identities=27% Similarity=0.583 Sum_probs=37.9
Q ss_pred ccCCCCCCcccccCCCCCcccccccCc------cccccCCCCcccCCCCCC
Q 036141 163 SKGRDMRQVQCFSCKEYRHIVVKCAKK------FCNYCKKPGHIIKECPTR 207 (220)
Q Consensus 163 ~~~~~~~~~~~~~~~~~g~~~~~~~~~------~C~~Cgk~GH~~~~C~~k 207 (220)
+..+...+..|..|+..||+.-.|+.. .|++||-.||++.+|+..
T Consensus 254 gt~r~~d~~~c~~cg~~~H~q~~cp~r~~~~~n~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 254 GTLRDDDNRACRNCGSTGHKQYDCPGRIPNTTNVCKICGPLGHISIDCKVN 304 (554)
T ss_pred CCCCccccccccccCCCccccccCCcccccccccccccCCcccccccCCCc
Confidence 444555567899999999998788765 899999999999999987
No 15
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=96.79 E-value=0.00081 Score=49.84 Aligned_cols=37 Identities=30% Similarity=0.798 Sum_probs=31.6
Q ss_pred cccccCCCCCcccccc-cC----ccccccCCCCcccCCCCCC
Q 036141 171 VQCFSCKEYRHIVVKC-AK----KFCNYCKKPGHIIKECPTR 207 (220)
Q Consensus 171 ~~~~~~~~~g~~~~~~-~~----~~C~~Cgk~GH~~~~C~~k 207 (220)
..|+.|+..||.+++| +. +.|+.|+..+|.+++||.-
T Consensus 98 ~~C~~Cg~~GH~~~dC~P~~~~~~~C~~C~s~~H~s~~Cp~~ 139 (190)
T COG5082 98 KKCYNCGETGHLSRDCNPSKDQQKSCFDCNSTRHSSEDCPSI 139 (190)
T ss_pred cccccccccCccccccCcccccCcceeccCCCccccccCccc
Confidence 6799999999999999 33 2699999999999999863
No 16
>PF03564 DUF1759: Protein of unknown function (DUF1759); InterPro: IPR005312 This is a small family of proteins of unknown function.
Probab=96.72 E-value=0.0093 Score=42.88 Aligned_cols=96 Identities=14% Similarity=0.162 Sum_probs=64.3
Q ss_pred cccccchHHHHhhcccc----ccHHHHHHHHHHHhccCChhHHhHHHHHHHHHh---c-CCccHHHHHHHHHHHHHHHhh
Q 036141 3 WIMGSIDQSLILNLKLH----KTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYS---Q-GNLSIQNYFSGFQNLWAEYVD 74 (220)
Q Consensus 3 ~i~~sl~~~~~~~~~~~----~ta~~~w~~L~~~f~~~~~~~~~~l~~~~~~~~---q-~~~sv~~y~~~~~~l~~~L~~ 74 (220)
+|...|..+-...|..+ .+-..+|..|+++|+...... ..+..++.... + +...+..+++.+..++..|..
T Consensus 33 ~L~~~L~G~A~~~i~~~~~~~~~Y~~a~~~L~~~yg~~~~i~-~~~~~~l~~l~~~~~~d~~~L~~~~~~v~~~i~~L~~ 111 (145)
T PF03564_consen 33 YLRSCLKGEAKELIRGLPLSEENYEEAWELLEERYGNPRRII-QALLEELRNLPPISNDDPEALRSLVDKVNNCIRALKA 111 (145)
T ss_pred HHHHHhcchHHHHHHcccccchhhHHHHHHHHHHhCCchHHH-HHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHHH
Confidence 34455555555555543 456899999999999654322 33344444444 2 368899999999999999997
Q ss_pred cccccCCcccHHHHHHHHHHHHHHHHHhhccchHHHH
Q 036141 75 MIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAA 111 (220)
Q Consensus 75 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~gLp~~~~~~ 111 (220)
+ |..+.+ ...+..|+..||+....-
T Consensus 112 l-g~~~~~-----------~~l~~~i~~KLp~~~~~~ 136 (145)
T PF03564_consen 112 L-GVNVDD-----------PLLISIILSKLPPEIREK 136 (145)
T ss_pred c-CCCCCC-----------HHHHHHHHHHCCHHHHHH
Confidence 6 765543 334555999999874443
No 17
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=96.62 E-value=0.00066 Score=39.30 Aligned_cols=17 Identities=53% Similarity=1.110 Sum_probs=16.0
Q ss_pred cccccCCCCcccCCCCC
Q 036141 190 FCNYCKKPGHIIKECPT 206 (220)
Q Consensus 190 ~C~~Cgk~GH~~~~C~~ 206 (220)
.|++||..||...+||.
T Consensus 33 ~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 33 FCFHCGRIGHSDKECPK 49 (49)
T ss_pred hhcCCCCcCcCHhHcCC
Confidence 79999999999999984
No 18
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=96.56 E-value=0.0023 Score=34.80 Aligned_cols=23 Identities=30% Similarity=0.554 Sum_probs=18.9
Q ss_pred ccccccCCCCccc--CCCCCCCCCC
Q 036141 189 KFCNYCKKPGHII--KECPTRPQNC 211 (220)
Q Consensus 189 ~~C~~Cgk~GH~~--~~C~~k~~~~ 211 (220)
.+|..||..||.. +.||.+....
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~~~~~ 26 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMYCWSG 26 (40)
T ss_pred ccccccccccccccCccCCCCCCCC
Confidence 3799999999998 6799887553
No 19
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=95.71 E-value=0.0092 Score=26.72 Aligned_cols=17 Identities=47% Similarity=1.065 Sum_probs=15.1
Q ss_pred ccccCCCCCcccccccC
Q 036141 172 QCFSCKEYRHIVVKCAK 188 (220)
Q Consensus 172 ~~~~~~~~g~~~~~~~~ 188 (220)
.|++|++.||.+++|++
T Consensus 2 ~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCPK 18 (18)
T ss_dssp BCTTTSCSSSCGCTSSS
T ss_pred cCcCCCCcCcccccCcc
Confidence 59999999999988874
No 20
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=95.64 E-value=0.0046 Score=48.73 Aligned_cols=20 Identities=45% Similarity=0.833 Sum_probs=17.9
Q ss_pred ccccccCCCCcccCCCCCCC
Q 036141 189 KFCNYCKKPGHIIKECPTRP 208 (220)
Q Consensus 189 ~~C~~Cgk~GH~~~~C~~k~ 208 (220)
..|+.|||.|||.++||...
T Consensus 161 ~~cyrcGkeghwskEcP~~~ 180 (346)
T KOG0109|consen 161 SGCYRCGKEGHWSKECPVDR 180 (346)
T ss_pred HHheeccccccccccCCccC
Confidence 37999999999999999754
No 21
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=95.02 E-value=0.019 Score=45.67 Aligned_cols=45 Identities=29% Similarity=0.745 Sum_probs=35.9
Q ss_pred CCCCcccccCCCCCccccccc--CccccccCCCCcccCCCCCCCCCC
Q 036141 167 DMRQVQCFSCKEYRHIVVKCA--KKFCNYCKKPGHIIKECPTRPQNC 211 (220)
Q Consensus 167 ~~~~~~~~~~~~~g~~~~~~~--~~~C~~Cgk~GH~~~~C~~k~~~~ 211 (220)
......|..|+..+|....|. ...|++|+..||++++|+......
T Consensus 69 ~~~~~~c~~~g~~~~~~~~~~~~~~~c~~C~~~gH~~~~c~~~~~~~ 115 (261)
T KOG4400|consen 69 ECPEVSCYICGEKGHLGRRCTRIAAACFNCGEGGHIERDCPEAGKEG 115 (261)
T ss_pred CCCCceeeecCCCCchhhcCcccchhhhhCCCCccchhhCCcccCcc
Confidence 345667999999998877766 468999999999999999876554
No 22
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=94.89 E-value=0.013 Score=46.36 Aligned_cols=22 Identities=36% Similarity=0.856 Sum_probs=19.0
Q ss_pred ccccccCCCCcccCCCCCCCCC
Q 036141 189 KFCNYCKKPGHIIKECPTRPQN 210 (220)
Q Consensus 189 ~~C~~Cgk~GH~~~~C~~k~~~ 210 (220)
-.||.||..|||...||..++.
T Consensus 177 Y~CyRCGqkgHwIqnCpTN~Dp 198 (427)
T COG5222 177 YVCYRCGQKGHWIQNCPTNQDP 198 (427)
T ss_pred eeEEecCCCCchhhcCCCCCCC
Confidence 3799999999999999976643
No 23
>PF02023 SCAN: SCAN domain; InterPro: IPR003309 A number of C2H2-zinc finger proteins contain a highly conserved N-terminal motif termed the SCAN domain. The SCAN domain may play an important role in the assembly and function of this newly defined subclass of transcriptional regulators [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3LHR_B 4E6S_A 2FI2_A 1Y7Q_A.
Probab=90.63 E-value=3.6 Score=27.31 Aligned_cols=79 Identities=15% Similarity=0.197 Sum_probs=50.7
Q ss_pred HHHHHHHh-cCCccHHHHHHHHHHHHHHHhhcccccCCcccHHHHHHHHHHHHHHHHHhhccchHHHHHHhhcCCCCCCC
Q 036141 45 EYEIARYS-QGNLSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRDLSPS 123 (220)
Q Consensus 45 ~~~~~~~~-q~~~sv~~y~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~gLp~~~~~~~~~l~~~~~~~s 123 (220)
++.|.... +.+++..+++.++..|+.+=-. + .+ ....++.|-..+.+||..||++....+. ... .-|
T Consensus 6 r~~FR~~~~~~~~~p~e~~~rL~~l~~~WL~--p-e~-----~tkeqi~ellvlEQFL~~lP~e~~~wV~---e~~-p~s 73 (95)
T PF02023_consen 6 RQRFRSFQYQEGEGPREFLSRLRELCDRWLQ--P-EV-----HTKEQILELLVLEQFLNILPPEVQTWVR---ERK-PES 73 (95)
T ss_dssp HHHHHT--CCTTTSHHHHHHHHHHHHHHHH---T-TT-----S-HHHHHHHHHHHHHHHHS-HHHHHHHH---TCS--SS
T ss_pred HHHHhCCCCCCCCCHHHHHHHHHHHHHHhCc--c-cc-----CcHHHHHHHHHHHHHHHHCCHHHHHHHH---hcC-CCC
Confidence 44576666 4589999999999999877631 2 11 1123346777789999999998665533 333 348
Q ss_pred HHHHHHHHHHHH
Q 036141 124 LDVCFKELLREE 135 (220)
Q Consensus 124 l~e~~~~l~~~e 135 (220)
.++++..+....
T Consensus 74 ~~ea~~Lae~~~ 85 (95)
T PF02023_consen 74 AEEAVALAEDYQ 85 (95)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 888877765544
No 24
>PF00607 Gag_p24: gag gene protein p24 (core nucleocapsid protein); InterPro: IPR000721 The Gag protein from retroviruses, also known as p24, forms the inner protein layer of the nucleocapsid. This protein performs highly complex orchestrated tasks during the assembly, budding, maturation and infection stages of the viral replication cycle. During viral assembly, the proteins form membrane associations and self-associations that ultimately result in budding of an immature virion from the infected cell. Gag precursors also function during viral assembly to selectively bind and package two plus strands of genomic RNA. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.; GO: 0016032 viral reproduction; PDB: 1BMX_A 1SJH_C 1SJE_C 1U57_A 1FGL_B 1G03_A 2XT1_A 2JO0_A 2L6E_A 2HJL_C ....
Probab=84.83 E-value=5.3 Score=30.59 Aligned_cols=40 Identities=15% Similarity=0.287 Sum_probs=29.1
Q ss_pred cHHHHHHHHHHHhccCChhHHhHHHHHHHHHhcC-CccHHHHHHHHHHHH
Q 036141 21 TAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQG-NLSIQNYFSGFQNLW 69 (220)
Q Consensus 21 ta~~~w~~L~~~f~~~~~~~~~~l~~~~~~~~q~-~~sv~~y~~~~~~l~ 69 (220)
-+-..|..|...+.+... |...+|| +|+..+|++||..-+
T Consensus 107 ~ai~Aw~~l~~~~~~~~~---------~~~I~QGp~Epf~dFv~rl~~a~ 147 (206)
T PF00607_consen 107 WAIKAWRKLPRKGSPGES---------FTKIKQGPKEPFADFVDRLQKAI 147 (206)
T ss_dssp HHHHHHHHHHHHHSSSST---------GGGH-S-TTSHHHHHHHHHHHHH
T ss_pred HHHHhhhccccccccccc---------HHHhhhccccchHHHHHHHHHHH
Confidence 455788899888886532 4456788 999999999998664
No 25
>PF14893 PNMA: PNMA
Probab=83.84 E-value=17 Score=30.10 Aligned_cols=53 Identities=23% Similarity=0.330 Sum_probs=41.8
Q ss_pred cccHHHHHHHHHHHhccCChhHHhHHHHHHHHHhc-CCccHHHHHHHHHHHHHHHh
Q 036141 19 HKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQ-GNLSIQNYFSGFQNLWAEYV 73 (220)
Q Consensus 19 ~~ta~~~w~~L~~~f~~~~~~~~~~l~~~~~~~~q-~~~sv~~y~~~~~~l~~~L~ 73 (220)
..|+.+..+.|...|..+.. ...+..+|..+.| .+|+|.+|+.++..++++.-
T Consensus 229 ~~t~~~~l~aL~~~Fg~~es--~~~~~~kf~~~~Q~~~E~ls~yv~RlE~lLqkav 282 (331)
T PF14893_consen 229 KQTAQDCLKALGQVFGSSES--RETLEAKFLNTFQEPGEKLSAYVKRLESLLQKAV 282 (331)
T ss_pred CCCHHHHHHHHHHhcCCccc--HHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHH
Confidence 45888999999999985544 3455666766666 59999999999999999863
No 26
>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]
Probab=83.77 E-value=0.37 Score=40.19 Aligned_cols=23 Identities=39% Similarity=0.806 Sum_probs=19.5
Q ss_pred ccccccCCCCcccCCCCCCCCCC
Q 036141 189 KFCNYCKKPGHIIKECPTRPQNC 211 (220)
Q Consensus 189 ~~C~~Cgk~GH~~~~C~~k~~~~ 211 (220)
+.|-|||-.||...+||+....+
T Consensus 571 kGCayCgGLGHRItdCPKle~~~ 593 (610)
T KOG0341|consen 571 KGCAYCGGLGHRITDCPKLEAQQ 593 (610)
T ss_pred cccccccCCCcccccCchhhhhc
Confidence 36999999999999999876443
No 27
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.63 E-value=0.75 Score=39.14 Aligned_cols=38 Identities=34% Similarity=0.791 Sum_probs=29.0
Q ss_pred cccccCCCCCcccccccC-------ccccccCCCCcccCCCCCCC
Q 036141 171 VQCFSCKEYRHIVVKCAK-------KFCNYCKKPGHIIKECPTRP 208 (220)
Q Consensus 171 ~~~~~~~~~g~~~~~~~~-------~~C~~Cgk~GH~~~~C~~k~ 208 (220)
..|..|...+|+...+.. .+|+.|+.+|||...||.-.
T Consensus 134 ~~~~~~~~~~~~iq~~~~~g~Pppsy~c~rc~~~g~wikacptv~ 178 (448)
T KOG0314|consen 134 YVCHRCNSPGHFIQHCSTNGSPPPSYKCVKCPTPGPWIKACPTVS 178 (448)
T ss_pred ceeeecccCccccccccccCCCCCCcceecCCCCCccceeccccC
Confidence 347777777777665443 38999999999999998644
No 28
>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes. Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.
Probab=83.09 E-value=0.64 Score=32.72 Aligned_cols=20 Identities=35% Similarity=0.776 Sum_probs=16.8
Q ss_pred CccccccCCCCcccCCCCCCC
Q 036141 188 KKFCNYCKKPGHIIKECPTRP 208 (220)
Q Consensus 188 ~~~C~~Cgk~GH~~~~C~~k~ 208 (220)
...|.+|+ -.||...||-|-
T Consensus 106 ~v~CR~Ck-GdH~T~~CPyKd 125 (128)
T PF12353_consen 106 KVKCRICK-GDHWTSKCPYKD 125 (128)
T ss_pred eEEeCCCC-CCcccccCCccc
Confidence 34799996 999999999764
No 29
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=81.30 E-value=1.1 Score=40.98 Aligned_cols=40 Identities=23% Similarity=0.554 Sum_probs=27.2
Q ss_pred CcccccCCCCCcccccc----------cCccccccCCCCcccCCCCCCCCC
Q 036141 170 QVQCFSCKEYRHIVVKC----------AKKFCNYCKKPGHIIKECPTRPQN 210 (220)
Q Consensus 170 ~~~~~~~~~~g~~~~~~----------~~~~C~~Cgk~GH~~~~C~~k~~~ 210 (220)
...|..||..-.- +.| ....|||||........||.--..
T Consensus 435 ~l~C~~Cg~v~~C-p~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 435 LLLCRDCGYIAEC-PNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred eeecccCCCcccC-CCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 3447777664432 122 233899999999999999986544
No 30
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=77.57 E-value=1.1 Score=40.56 Aligned_cols=20 Identities=35% Similarity=0.898 Sum_probs=17.9
Q ss_pred cccccCCCCcccCCCCCCCC
Q 036141 190 FCNYCKKPGHIIKECPTRPQ 209 (220)
Q Consensus 190 ~C~~Cgk~GH~~~~C~~k~~ 209 (220)
.|+.||..||.+++|.-+..
T Consensus 262 ~C~~cgq~gh~~~dc~g~~~ 281 (931)
T KOG2044|consen 262 RCFLCGQTGHEAKDCEGKPR 281 (931)
T ss_pred cchhhcccCCcHhhcCCcCC
Confidence 69999999999999987743
No 31
>KOG2560 consensus RNA splicing factor - Slu7p [RNA processing and modification]
Probab=72.49 E-value=0.67 Score=39.21 Aligned_cols=27 Identities=33% Similarity=0.674 Sum_probs=21.6
Q ss_pred cCccccccCCCCcccCCCCCCCCCCcC
Q 036141 187 AKKFCNYCKKPGHIIKECPTRPQNCQA 213 (220)
Q Consensus 187 ~~~~C~~Cgk~GH~~~~C~~k~~~~~~ 213 (220)
..+-|-+||--||-.++|..++.+.++
T Consensus 111 RKGACeNCGAmtHk~KDCmERPRK~gA 137 (529)
T KOG2560|consen 111 RKGACENCGAMTHKVKDCMERPRKVGA 137 (529)
T ss_pred hhhhhhhhhhhhcchHHHhhcchhhcc
Confidence 344799999999999999877765543
No 32
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=72.32 E-value=2.1 Score=36.36 Aligned_cols=20 Identities=25% Similarity=0.654 Sum_probs=17.6
Q ss_pred ccccCCCCcccCCCCCCCCC
Q 036141 191 CNYCKKPGHIIKECPTRPQN 210 (220)
Q Consensus 191 C~~Cgk~GH~~~~C~~k~~~ 210 (220)
||+||-.-|-.++||..+..
T Consensus 131 CFNC~g~~hsLrdC~rp~d~ 150 (485)
T KOG2673|consen 131 CFNCGGTPHSLRDCPRPFDF 150 (485)
T ss_pred ccccCCCCCccccCCCcccc
Confidence 99999999999999976643
No 33
>COG2879 Uncharacterized small protein [Function unknown]
Probab=71.52 E-value=13 Score=22.47 Aligned_cols=31 Identities=10% Similarity=0.292 Sum_probs=23.2
Q ss_pred HHHhhccchHHHHHHhhcC---CCCCCCHHHHHHH
Q 036141 99 QFLMKLRPKYEAARSNLMN---RDLSPSLDVCFKE 130 (220)
Q Consensus 99 ~~l~gLp~~~~~~~~~l~~---~~~~~sl~e~~~~ 130 (220)
+++.|+|+ |+..+..+.. ..+..|.+|+...
T Consensus 17 ~lmvGvpd-YdnYVehmr~~hPd~p~mT~~EFfre 50 (65)
T COG2879 17 KLMVGVPD-YDNYVEHMRKKHPDKPPMTYEEFFRE 50 (65)
T ss_pred HHHcCCCc-HHHHHHHHHHhCcCCCcccHHHHHHH
Confidence 38999987 9999988866 4556677777654
No 34
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=69.73 E-value=16 Score=26.39 Aligned_cols=30 Identities=13% Similarity=0.242 Sum_probs=19.9
Q ss_pred CCCcccccCCCCCcccccccCccccccCCC
Q 036141 168 MRQVQCFSCKEYRHIVVKCAKKFCNYCKKP 197 (220)
Q Consensus 168 ~~~~~~~~~~~~g~~~~~~~~~~C~~Cgk~ 197 (220)
.|...|-+|+..-+......=+.|..||..
T Consensus 110 ~G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 110 PGTLVCENCGHEVELTHPERLPPCPKCGHT 139 (146)
T ss_pred CceEecccCCCEEEecCCCcCCCCCCCCCC
Confidence 445568888887766443344578888764
No 35
>KOG4602 consensus Nanos and related proteins [General function prediction only]
Probab=69.63 E-value=4.3 Score=31.81 Aligned_cols=46 Identities=30% Similarity=0.615 Sum_probs=29.8
Q ss_pred cCCCCCCcccccCCCCCcc--------ccc------ccCc---cccccCCCC---cccCCCCCCCC
Q 036141 164 KGRDMRQVQCFSCKEYRHI--------VVK------CAKK---FCNYCKKPG---HIIKECPTRPQ 209 (220)
Q Consensus 164 ~~~~~~~~~~~~~~~~g~~--------~~~------~~~~---~C~~Cgk~G---H~~~~C~~k~~ 209 (220)
++...+..-|..|...+.. .+. |+.. .|-.||-.| |+.+.||....
T Consensus 227 pg~Q~r~l~CvFC~nN~E~~A~y~tH~lkd~dgRVLCPkLR~YVCPiCGATgDnAHTiKyCPl~~~ 292 (318)
T KOG4602|consen 227 PGNQPRPLCCVFCFNNAEEFARYHTHPLKDKDGRVLCPKLRSYVCPICGATGDNAHTIKYCPLAFG 292 (318)
T ss_pred CCCCCCceeEEeecCCCchhhheecccccCCCCcEechhHhhhcCccccccCCcccceecccccCC
Confidence 3334445568888877633 221 3332 699998776 99999998663
No 36
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=66.13 E-value=3.3 Score=30.68 Aligned_cols=16 Identities=38% Similarity=0.949 Sum_probs=14.1
Q ss_pred ccccCCCCcccCCCCC
Q 036141 191 CNYCKKPGHIIKECPT 206 (220)
Q Consensus 191 C~~Cgk~GH~~~~C~~ 206 (220)
|++||..||+.+.|.+
T Consensus 103 ~~r~G~rg~~~r~~~~ 118 (195)
T KOG0107|consen 103 CYRCGERGHIGRNCKD 118 (195)
T ss_pred cccCCCcccccccccc
Confidence 8899999999998876
No 37
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=63.55 E-value=3 Score=21.38 Aligned_cols=26 Identities=15% Similarity=0.220 Sum_probs=13.5
Q ss_pred cccccCCCCCcccccccCccccccCC
Q 036141 171 VQCFSCKEYRHIVVKCAKKFCNYCKK 196 (220)
Q Consensus 171 ~~~~~~~~~g~~~~~~~~~~C~~Cgk 196 (220)
.-|..||.+-......+...|..||.
T Consensus 4 rfC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 4 RFCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp SB-TTT--BEEE-SSSS-EEESSSS-
T ss_pred cccCcCCccccCCCCcCEeECCCCcC
Confidence 34777777766665666667777764
No 38
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=63.38 E-value=4.9 Score=19.54 Aligned_cols=22 Identities=27% Similarity=0.558 Sum_probs=12.5
Q ss_pred ccccCCCCCcccccccCccccccCCC
Q 036141 172 QCFSCKEYRHIVVKCAKKFCNYCKKP 197 (220)
Q Consensus 172 ~~~~~~~~g~~~~~~~~~~C~~Cgk~ 197 (220)
.|.+|+..- ......|.+||.+
T Consensus 4 ~Cp~Cg~~~----~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 4 FCPNCGAEI----DPDAKFCPNCGAK 25 (26)
T ss_pred CCcccCCcC----CcccccChhhCCC
Confidence 366666632 2234568888764
No 39
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=62.47 E-value=5.8 Score=19.06 Aligned_cols=8 Identities=25% Similarity=0.384 Sum_probs=5.6
Q ss_pred ccccccCC
Q 036141 189 KFCNYCKK 196 (220)
Q Consensus 189 ~~C~~Cgk 196 (220)
..|.+||+
T Consensus 17 f~CPnCG~ 24 (24)
T PF07754_consen 17 FPCPNCGF 24 (24)
T ss_pred EeCCCCCC
Confidence 46888874
No 40
>TIGR03859 PQQ_PqqD coenzyme PQQ biosynthesis protein PqqD. This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ.
Probab=61.65 E-value=32 Score=21.87 Aligned_cols=31 Identities=3% Similarity=0.087 Sum_probs=23.8
Q ss_pred cccchHHHHhhccccccHHHHHHHHHHHhcc
Q 036141 5 MGSIDQSLILNLKLHKTAKDMWEYLKKVYNQ 35 (220)
Q Consensus 5 ~~sl~~~~~~~~~~~~ta~~~w~~L~~~f~~ 35 (220)
++.+.-.|...+....|..++|..|.+.|..
T Consensus 29 Ln~~g~~Iw~lldg~~tv~eI~~~L~~~Y~~ 59 (81)
T TIGR03859 29 LNDSAGEILELCDGKRSLAEIIQELAQRFPA 59 (81)
T ss_pred eChHHHHHHHHccCCCcHHHHHHHHHHHcCC
Confidence 3455667778888888888888888888875
No 41
>PF07904 Eaf7: Chromatin modification-related protein EAF7; InterPro: IPR012423 The Saccharomyces cerevisiae (Baker's yeast) member of this family P53911 from SWISSPROT is part of NuA4, the only essential histone acetyltransferase complex in S. cerevisiae involved in global histone acetylation []. ; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus, 0043189 H4/H2A histone acetyltransferase complex
Probab=61.59 E-value=7.6 Score=25.52 Aligned_cols=29 Identities=31% Similarity=0.486 Sum_probs=22.9
Q ss_pred ccchHHHHhh-----ccccccHHHHHHHHHHHhc
Q 036141 6 GSIDQSLILN-----LKLHKTAKDMWEYLKKVYN 34 (220)
Q Consensus 6 ~sl~~~~~~~-----~~~~~ta~~~w~~L~~~f~ 34 (220)
..|...+... +...-|+.++|+.|...|.
T Consensus 25 ~~I~~~l~~~~~~~~~~~~~t~~~IW~kL~~~Yd 58 (91)
T PF07904_consen 25 ICIVERLNNPGFDPKLNKHFTIDDIWKKLRTLYD 58 (91)
T ss_pred HHHHHHHhccccCCccCCcCCHHHHHHHHHHhcC
Confidence 3455556666 7778899999999999997
No 42
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=60.46 E-value=4.9 Score=22.53 Aligned_cols=26 Identities=19% Similarity=0.402 Sum_probs=15.4
Q ss_pred ccccCCCCCcccccccCccccccCCC
Q 036141 172 QCFSCKEYRHIVVKCAKKFCNYCKKP 197 (220)
Q Consensus 172 ~~~~~~~~g~~~~~~~~~~C~~Cgk~ 197 (220)
.|.+||..-.........+|.+||.+
T Consensus 5 ~C~~CG~~~~~~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 5 KCARCGREVELDEYGTGVRCPYCGYR 30 (46)
T ss_pred ECCCCCCEEEECCCCCceECCCCCCe
Confidence 36666665544333335689999753
No 43
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=60.40 E-value=6.4 Score=24.07 Aligned_cols=29 Identities=14% Similarity=0.149 Sum_probs=20.1
Q ss_pred cccccCCCCCcccccccCccccccCCCCc
Q 036141 171 VQCFSCKEYRHIVVKCAKKFCNYCKKPGH 199 (220)
Q Consensus 171 ~~~~~~~~~g~~~~~~~~~~C~~Cgk~GH 199 (220)
..|+.||.............|..||...|
T Consensus 29 q~C~~CG~~~~~~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 29 QTCPRCGHRNKKRRSGRVFTCPNCGFEMD 57 (69)
T ss_pred cCccCcccccccccccceEEcCCCCCEEC
Confidence 45888888777634444558999987655
No 44
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=60.08 E-value=6.4 Score=18.59 Aligned_cols=10 Identities=50% Similarity=1.235 Sum_probs=6.9
Q ss_pred CccccccCCC
Q 036141 188 KKFCNYCKKP 197 (220)
Q Consensus 188 ~~~C~~Cgk~ 197 (220)
...|.+||.+
T Consensus 13 ~~fC~~CG~~ 22 (23)
T PF13240_consen 13 AKFCPNCGTP 22 (23)
T ss_pred CcchhhhCCc
Confidence 3468888864
No 45
>KOG3794 consensus CBF1-interacting corepressor CIR and related proteins [Transcription]
Probab=58.62 E-value=4.2 Score=33.88 Aligned_cols=21 Identities=43% Similarity=0.725 Sum_probs=16.2
Q ss_pred CccccccCCCCccc--CCCCCCC
Q 036141 188 KKFCNYCKKPGHII--KECPTRP 208 (220)
Q Consensus 188 ~~~C~~Cgk~GH~~--~~C~~k~ 208 (220)
+..|..|++-||+. ++||-.-
T Consensus 124 NVrC~kChkwGH~n~DreCplf~ 146 (453)
T KOG3794|consen 124 NVRCLKCHKWGHINTDRECPLFG 146 (453)
T ss_pred eeeEEeecccccccCCccCcchh
Confidence 44799999999986 5688643
No 46
>PRK14873 primosome assembly protein PriA; Provisional
Probab=57.34 E-value=7 Score=35.60 Aligned_cols=22 Identities=18% Similarity=0.517 Sum_probs=16.3
Q ss_pred CccccccCCCCcccCCCCCCCCC
Q 036141 188 KKFCNYCKKPGHIIKECPTRPQN 210 (220)
Q Consensus 188 ~~~C~~Cgk~GH~~~~C~~k~~~ 210 (220)
...|++||..- .-..||.-...
T Consensus 410 ~l~Ch~CG~~~-~p~~Cp~Cgs~ 431 (665)
T PRK14873 410 TPRCRWCGRAA-PDWRCPRCGSD 431 (665)
T ss_pred eeECCCCcCCC-cCccCCCCcCC
Confidence 34799999875 67889976543
No 47
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=56.72 E-value=8.3 Score=33.89 Aligned_cols=22 Identities=36% Similarity=0.676 Sum_probs=17.8
Q ss_pred CccccccCCCCcccCCCCCCCC
Q 036141 188 KKFCNYCKKPGHIIKECPTRPQ 209 (220)
Q Consensus 188 ~~~C~~Cgk~GH~~~~C~~k~~ 209 (220)
...|++||..-=+-..||.-..
T Consensus 240 ~l~Ch~Cg~~~~~~~~Cp~C~s 261 (505)
T TIGR00595 240 KLRCHYCGYQEPIPKTCPQCGS 261 (505)
T ss_pred eEEcCCCcCcCCCCCCCCCCCC
Confidence 3479999988888889997654
No 48
>PF15616 TerY-C: TerY-C metal binding domain
Probab=55.59 E-value=8.5 Score=27.16 Aligned_cols=34 Identities=21% Similarity=0.484 Sum_probs=23.0
Q ss_pred CCcccccCCCCCccc-ccccCc---------cccccCCCCcccC
Q 036141 169 RQVQCFSCKEYRHIV-VKCAKK---------FCNYCKKPGHIIK 202 (220)
Q Consensus 169 ~~~~~~~~~~~g~~~-~~~~~~---------~C~~Cgk~GH~~~ 202 (220)
+.+.|.+|+..-... =.|.+. .|.+||+.|.+..
T Consensus 76 g~PgCP~CGn~~~fa~C~CGkl~Ci~g~~~~~CPwCg~~g~~~~ 119 (131)
T PF15616_consen 76 GAPGCPHCGNQYAFAVCGCGKLFCIDGEGEVTCPWCGNEGSFGA 119 (131)
T ss_pred CCCCCCCCcChhcEEEecCCCEEEeCCCCCEECCCCCCeeeecc
Confidence 346799999884332 244443 7889999988754
No 49
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=53.45 E-value=47 Score=19.89 Aligned_cols=23 Identities=17% Similarity=0.172 Sum_probs=8.5
Q ss_pred HHHhhccccccHHHHHHHHHHHh
Q 036141 11 SLILNLKLHKTAKDMWEYLKKVY 33 (220)
Q Consensus 11 ~~~~~~~~~~ta~~~w~~L~~~f 33 (220)
.|+..+..-.|..++.+.|.+.|
T Consensus 21 ~Iw~~~~g~~t~~ei~~~l~~~y 43 (68)
T PF05402_consen 21 FIWELLDGPRTVEEIVDALAEEY 43 (68)
T ss_dssp HHHHH--SSS-HHHHHHHHHHHT
T ss_pred HHHHHccCCCCHHHHHHHHHHHc
Confidence 33344433344444444444444
No 50
>TIGR02642 phage_xxxx uncharacterized phage protein. This uncharacterized protein is found in prophage regions of Shewanella oneidensis MR-1, Vibrio vulnificus YJ016, Yersinia pseudotuberculosis IP 32953, and Aeromonas hydrophila ATCC7966. It appears to have regions of sequence similarity to phage lambda antitermination protein Q.
Probab=53.24 E-value=8.5 Score=28.97 Aligned_cols=31 Identities=19% Similarity=0.479 Sum_probs=22.2
Q ss_pred CcccccCCCCCcccccccCccccccCCCCcccC
Q 036141 170 QVQCFSCKEYRHIVVKCAKKFCNYCKKPGHIIK 202 (220)
Q Consensus 170 ~~~~~~~~~~g~~~~~~~~~~C~~Cgk~GH~~~ 202 (220)
...|..|++.|...+.. ..|..|+-.|+...
T Consensus 99 ~~~C~~C~G~G~~i~~~--~~C~~C~G~G~v~~ 129 (186)
T TIGR02642 99 SCKCPRCRGTGLIQRRQ--RECDTCAGTGRFRP 129 (186)
T ss_pred CCcCCCCCCeeEEecCC--CCCCCCCCccEEee
Confidence 34699999988774322 46999988887653
No 51
>PF00684 DnaJ_CXXCXGXG: DnaJ central domain; InterPro: IPR001305 The hsp70 chaperone machine performs many diverse roles in the cell, including folding of nascent proteins, translocation of polypeptides across organelle membranes, coordinating responses to stress, and targeting selected proteins for degradation. DnaJ is a member of the hsp40 family of molecular chaperones, which is also called the J-protein family, the members of which regulate the activity of hsp70s. DnaJ (hsp40) binds to DnaK (hsp70) and stimulates its ATPase activity, generating the ADP-bound state of DnaK, which interacts stably with the polypeptide substrate []. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation []. DnaJ consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acid residues, a glycine and phenylalanine-rich domain ('G/F' domain), a central cysteine rich domain (CR-type zinc finger) containing four repeats of a CXXCXGXG motif which can coordinate two zinc atom and a C-terminal domain (CTD) []. This entry represents the central cysteine-rich (CR) domain of DnaJ proteins. This central cysteine rich domain (CR-type zinc finger) has an overall V-shaped extended beta-hairpin topology and contains four repeats of the motif CXXCXGXG where X is any amino acid. The isolated cysteine rich domain folds in zinc dependent fashion. Each set of two repeats binds one unit of zinc. Although this domain has been implicated in substrate binding, no evidence of specific interaction between the isolated DnaJ cysteine rich domain and various hydrophobic peptides has been found [].; GO: 0031072 heat shock protein binding, 0051082 unfolded protein binding; PDB: 1NLT_A 2CTT_A 1EXK_A.
Probab=52.92 E-value=16 Score=22.26 Aligned_cols=41 Identities=22% Similarity=0.517 Sum_probs=25.2
Q ss_pred CCCCcccccCCCCCccccccc--------CccccccCCCCccc--CCCCCC
Q 036141 167 DMRQVQCFSCKEYRHIVVKCA--------KKFCNYCKKPGHII--KECPTR 207 (220)
Q Consensus 167 ~~~~~~~~~~~~~g~~~~~~~--------~~~C~~Cgk~GH~~--~~C~~k 207 (220)
......|..|+..|....... ...|..|+-.|.+. ..|+.=
T Consensus 12 ~~~~~~C~~C~G~G~~~~~~~~~~~~~~~~~~C~~C~G~G~~i~~~~C~~C 62 (66)
T PF00684_consen 12 GKKPKTCPQCNGSGQVTRRQQTPGGVFQMQQTCPKCGGTGKIIEKDPCKTC 62 (66)
T ss_dssp TTT-EE-TTSSSSSEEEEEEESSSTTEEEEEE-TTTSSSSEE-TSSB-SSS
T ss_pred CCCCcCCcCCCCeeEEEEEEeCCCeEEEEEEECCCCcceeeEECCCCCCCC
Confidence 344557999999998754331 23799999999984 556653
No 52
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=52.20 E-value=11 Score=22.40 Aligned_cols=19 Identities=42% Similarity=0.887 Sum_probs=15.1
Q ss_pred ccCccccccCCCCcccCCC
Q 036141 186 CAKKFCNYCKKPGHIIKEC 204 (220)
Q Consensus 186 ~~~~~C~~Cgk~GH~~~~C 204 (220)
|....|+.|+.+.|.-..|
T Consensus 46 C~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 46 CGFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred CCCeECCCCCCcCCCCCCC
Confidence 4456899999999987665
No 53
>PRK11032 hypothetical protein; Provisional
Probab=52.10 E-value=63 Score=23.70 Aligned_cols=30 Identities=13% Similarity=0.360 Sum_probs=19.8
Q ss_pred CCCcccccCCCCCcccccccCccccccCCC
Q 036141 168 MRQVQCFSCKEYRHIVVKCAKKFCNYCKKP 197 (220)
Q Consensus 168 ~~~~~~~~~~~~g~~~~~~~~~~C~~Cgk~ 197 (220)
.|...|-+|+..-+......=+.|..||..
T Consensus 122 ~G~LvC~~Cg~~~~~~~p~~i~pCp~C~~~ 151 (160)
T PRK11032 122 LGNLVCEKCHHHLAFYTPEVLPLCPKCGHD 151 (160)
T ss_pred cceEEecCCCCEEEecCCCcCCCCCCCCCC
Confidence 455668888887766444444578888754
No 54
>PRK05580 primosome assembly protein PriA; Validated
Probab=51.55 E-value=11 Score=34.45 Aligned_cols=22 Identities=27% Similarity=0.517 Sum_probs=17.4
Q ss_pred CccccccCCCCcccCCCCCCCC
Q 036141 188 KKFCNYCKKPGHIIKECPTRPQ 209 (220)
Q Consensus 188 ~~~C~~Cgk~GH~~~~C~~k~~ 209 (220)
...|++||..-=....||.-..
T Consensus 408 ~l~Ch~Cg~~~~~~~~Cp~Cg~ 429 (679)
T PRK05580 408 RLRCHHCGYQEPIPKACPECGS 429 (679)
T ss_pred eEECCCCcCCCCCCCCCCCCcC
Confidence 3479999988878888997654
No 55
>PRK11582 flagella biosynthesis protein FliZ; Provisional
Probab=50.98 E-value=59 Score=23.68 Aligned_cols=21 Identities=10% Similarity=0.199 Sum_probs=17.0
Q ss_pred cCCccHHHHHHHHHHHHHHHh
Q 036141 53 QGNLSIQNYFSGFQNLWAEYV 73 (220)
Q Consensus 53 q~~~sv~~y~~~~~~l~~~L~ 73 (220)
....+|.||+-|+++|=.=|.
T Consensus 102 MshSTvrEYVVRLRRLd~lL~ 122 (169)
T PRK11582 102 MSHSTVREYVVRLRRLDEHLH 122 (169)
T ss_pred cccccHHHHHHHHHHHHHHHh
Confidence 356799999999999966664
No 56
>TIGR03823 FliZ flagellar regulatory protein FliZ. FliZ is involved in the regulation of flagellar assembly and possibly also the down-regulation of the motile phenotype. FliZ interacts with the flagellar translational activator FlhCD complex.
Probab=50.18 E-value=56 Score=23.76 Aligned_cols=21 Identities=14% Similarity=0.234 Sum_probs=17.0
Q ss_pred cCCccHHHHHHHHHHHHHHHh
Q 036141 53 QGNLSIQNYFSGFQNLWAEYV 73 (220)
Q Consensus 53 q~~~sv~~y~~~~~~l~~~L~ 73 (220)
....+|.||+-|+++|=.=|.
T Consensus 102 MshStvrEYVVRLRRLd~lL~ 122 (168)
T TIGR03823 102 MSHSTVREYVVRLRRLDELLV 122 (168)
T ss_pred cccccHHHHHHHHHHHHHHHh
Confidence 356799999999999866564
No 57
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=49.54 E-value=17 Score=30.54 Aligned_cols=42 Identities=21% Similarity=0.455 Sum_probs=30.3
Q ss_pred CCcccccCCCCCcccccc------cCccccccCCCCcccC-CCCCCCCC
Q 036141 169 RQVQCFSCKEYRHIVVKC------AKKFCNYCKKPGHIIK-ECPTRPQN 210 (220)
Q Consensus 169 ~~~~~~~~~~~g~~~~~~------~~~~C~~Cgk~GH~~~-~C~~k~~~ 210 (220)
....|..|++.|...... .+..|..|+-.|++.. -|+.-+..
T Consensus 158 ~~~tC~tC~G~G~v~~~~~~g~~~~~~~C~~C~G~G~~i~~pC~~C~G~ 206 (371)
T COG0484 158 DPKTCPTCNGSGQVRTVQRTGFFSFQQTCPTCNGTGKIIKDPCGKCKGK 206 (371)
T ss_pred CCCcCCCCCCcCeEEEEEeeeEEEEEEECCCCccceeECCCCCCCCCCC
Confidence 466799999999765433 2237999999999884 47765543
No 58
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=49.19 E-value=4.5 Score=28.91 Aligned_cols=19 Identities=32% Similarity=0.754 Sum_probs=16.4
Q ss_pred cccccCCCCcccCCCCCCC
Q 036141 190 FCNYCKKPGHIIKECPTRP 208 (220)
Q Consensus 190 ~C~~Cgk~GH~~~~C~~k~ 208 (220)
.|..|=..|||..+|..+.
T Consensus 29 rCQKClq~GHWtYECk~kR 47 (177)
T KOG3116|consen 29 RCQKCLQAGHWTYECKNKR 47 (177)
T ss_pred hHHHHHhhccceeeecCce
Confidence 4999999999999997654
No 59
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=49.16 E-value=8.1 Score=34.43 Aligned_cols=21 Identities=29% Similarity=0.804 Sum_probs=16.5
Q ss_pred CccccccCCCCcccC--CCCCCC
Q 036141 188 KKFCNYCKKPGHIIK--ECPTRP 208 (220)
Q Consensus 188 ~~~C~~Cgk~GH~~~--~C~~k~ 208 (220)
..+|-+||..||+.- -||.-.
T Consensus 937 tr~C~nCGQvGHmkTNK~CP~f~ 959 (968)
T COG5179 937 TRTCGNCGQVGHMKTNKACPKFS 959 (968)
T ss_pred ceecccccccccccccccCcccc
Confidence 347999999999875 498754
No 60
>KOG3188 consensus Uncharacterized conserved protein [Function unknown]
Probab=49.01 E-value=1.1e+02 Score=23.52 Aligned_cols=27 Identities=15% Similarity=0.113 Sum_probs=20.9
Q ss_pred HHHhhccchHHHHHHhhcCCCCCCCHHHHH
Q 036141 99 QFLMKLRPKYEAARSNLMNRDLSPSLDVCF 128 (220)
Q Consensus 99 ~~l~gLp~~~~~~~~~l~~~~~~~sl~e~~ 128 (220)
.|+.|+ .++.++.++.+...++.+++.
T Consensus 23 m~liGi---lRhyvsiLl~s~kk~~~~~v~ 49 (246)
T KOG3188|consen 23 MFLIGI---LRHYVSILLQSSKKLEQEQVK 49 (246)
T ss_pred HHHHHH---HHHHHHHHHhcCCcccHHHhh
Confidence 378888 778888888887777777765
No 61
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=47.27 E-value=31 Score=27.93 Aligned_cols=19 Identities=21% Similarity=0.707 Sum_probs=15.7
Q ss_pred CcccccCCCCCcccccccC
Q 036141 170 QVQCFSCKEYRHIVVKCAK 188 (220)
Q Consensus 170 ~~~~~~~~~~g~~~~~~~~ 188 (220)
.-.|++||+.||+...|+.
T Consensus 176 gY~CyRCGqkgHwIqnCpT 194 (427)
T COG5222 176 GYVCYRCGQKGHWIQNCPT 194 (427)
T ss_pred ceeEEecCCCCchhhcCCC
Confidence 4459999999999887764
No 62
>PHA02540 61 DNA primase; Provisional
Probab=46.26 E-value=9.4 Score=31.61 Aligned_cols=31 Identities=16% Similarity=0.249 Sum_probs=19.7
Q ss_pred CcccccCCCCCcccc--------ccc--CccccccCCCCcc
Q 036141 170 QVQCFSCKEYRHIVV--------KCA--KKFCNYCKKPGHI 200 (220)
Q Consensus 170 ~~~~~~~~~~g~~~~--------~~~--~~~C~~Cgk~GH~ 200 (220)
...|..|+...|... ... .-+||.||..|-.
T Consensus 27 ~~~CPf~~ds~~~~~kpsF~V~p~k~~~~yhCFgCGa~Gd~ 67 (337)
T PHA02540 27 NFRCPICGDSQKDKNKARGWIYEKKDGGVFKCHNCGYHRPF 67 (337)
T ss_pred EecCCCCCCccccCcCCcEEEeccCCceEEEecCCCCCCCH
Confidence 346888888665311 111 2279999999854
No 63
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=45.99 E-value=17 Score=18.77 Aligned_cols=23 Identities=17% Similarity=0.346 Sum_probs=11.9
Q ss_pred cccCCCCCcccccccCccccccCC
Q 036141 173 CFSCKEYRHIVVKCAKKFCNYCKK 196 (220)
Q Consensus 173 ~~~~~~~g~~~~~~~~~~C~~Cgk 196 (220)
|..|+..... .......|.+||.
T Consensus 3 C~~Cg~~~~~-~~~~~irC~~CG~ 25 (32)
T PF03604_consen 3 CGECGAEVEL-KPGDPIRCPECGH 25 (32)
T ss_dssp ESSSSSSE-B-STSSTSSBSSSS-
T ss_pred CCcCCCeeEc-CCCCcEECCcCCC
Confidence 5556555443 2233457888874
No 64
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=44.42 E-value=12 Score=30.19 Aligned_cols=21 Identities=24% Similarity=0.604 Sum_probs=17.9
Q ss_pred CCcccccCCCCCcccccccCc
Q 036141 169 RQVQCFSCKEYRHIVVKCAKK 189 (220)
Q Consensus 169 ~~~~~~~~~~~g~~~~~~~~~ 189 (220)
.+.+|..||..||+.++|+..
T Consensus 159 Dq~~cyrcGkeghwskEcP~~ 179 (346)
T KOG0109|consen 159 DQSGCYRCGKEGHWSKECPVD 179 (346)
T ss_pred CHHHheeccccccccccCCcc
Confidence 356799999999999999863
No 65
>PF05310 Tenui_NS3: Tenuivirus movement protein; InterPro: IPR007974 This family of ssRNA negative-strand crop plant tenuivirus proteins appears to combine PV2 [], NS2 [], NS3, and PV3 proteins. Plant viruses encode specific proteins known as movement proteins (MPs) to control their spread through plasmodesmata (PD) in walls between cells as well as from leaf to leaf via vascular-dependent transport. During this movement process, the virally encoded MPs interact with viral genomes for transport from the viral replication sites to the PDs in the walls of infected cells along the cytoskeleton and/or endoplasmic reticulum (ER) network. The virus is then thought to move through the PDs in the form of MP-associated ribonucleoprotein complexes or as virions []. The NS3 protein appears to function as an RNA silencing suppressor [].; PDB: 3AJF_A.
Probab=43.39 E-value=7.8 Score=28.68 Aligned_cols=17 Identities=29% Similarity=0.538 Sum_probs=0.0
Q ss_pred cCccccccCCCCcccCC
Q 036141 187 AKKFCNYCKKPGHIIKE 203 (220)
Q Consensus 187 ~~~~C~~Cgk~GH~~~~ 203 (220)
++.+||.|.|+.|.+.+
T Consensus 97 ~~tKCWlCdk~~~~~t~ 113 (186)
T PF05310_consen 97 PKTKCWLCDKPSYQETD 113 (186)
T ss_dssp -----------------
T ss_pred CccceEEecchhhhccC
Confidence 34579999999998766
No 66
>PRK04023 DNA polymerase II large subunit; Validated
Probab=43.26 E-value=19 Score=34.16 Aligned_cols=37 Identities=22% Similarity=0.438 Sum_probs=19.7
Q ss_pred CcccccCCCCCccccccc---C-----ccccccCCCCcccCCCCCCC
Q 036141 170 QVQCFSCKEYRHIVVKCA---K-----KFCNYCKKPGHIIKECPTRP 208 (220)
Q Consensus 170 ~~~~~~~~~~g~~~~~~~---~-----~~C~~Cgk~GH~~~~C~~k~ 208 (220)
...|..||..+.. ..|+ . ..|..||+.+.- ..||+-.
T Consensus 626 ~RfCpsCG~~t~~-frCP~CG~~Te~i~fCP~CG~~~~~-y~CPKCG 670 (1121)
T PRK04023 626 RRKCPSCGKETFY-RRCPFCGTHTEPVYRCPRCGIEVEE-DECEKCG 670 (1121)
T ss_pred CccCCCCCCcCCc-ccCCCCCCCCCcceeCccccCcCCC-CcCCCCC
Confidence 5568888887532 2222 1 246666555553 3366544
No 67
>PF14684 Tricorn_C1: Tricorn protease C1 domain; PDB: 1N6F_D 1N6D_C 1N6E_C 1K32_A.
Probab=42.11 E-value=72 Score=19.57 Aligned_cols=52 Identities=4% Similarity=0.144 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHhccCChhH--HhHHHHHHHHHhcCCccHHHHHHHHHHHHHHHh
Q 036141 22 AKDMWEYLKKVYNQDNTAK--RSHLEYEIARYSQGNLSIQNYFSGFQNLWAEYV 73 (220)
Q Consensus 22 a~~~w~~L~~~f~~~~~~~--~~~l~~~~~~~~q~~~sv~~y~~~~~~l~~~L~ 73 (220)
..++|..+++.|-...... =..++.++.-....-.+-.++..-|..+..+|.
T Consensus 8 F~~~W~~~~~~f~d~~~~gvDW~~~~~~Y~p~v~~~~~~~el~~vl~eMl~eL~ 61 (70)
T PF14684_consen 8 FDEAWRLVRENFYDPDMHGVDWDAVYDRYRPLVPAAKTRDELYDVLNEMLGELN 61 (70)
T ss_dssp HHHHHHHHHHHSS-HHHHHHHHHHHHHHHHGGGGG--SHHHHHHHHHHHHHTT-
T ss_pred HHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHC
Confidence 4678998988886432211 133344455444555566777777777777765
No 68
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=40.25 E-value=16 Score=29.32 Aligned_cols=34 Identities=18% Similarity=0.240 Sum_probs=24.5
Q ss_pred cccccCCCCCcccccccCccccccCCCCcccCCCC
Q 036141 171 VQCFSCKEYRHIVVKCAKKFCNYCKKPGHIIKECP 205 (220)
Q Consensus 171 ~~~~~~~~~g~~~~~~~~~~C~~Cgk~GH~~~~C~ 205 (220)
.-|.+||.+...........|.+||.. ||-+-+|
T Consensus 112 RFCg~CG~~~~~~~~g~~~~C~~cg~~-~fPR~dP 145 (279)
T COG2816 112 RFCGRCGTKTYPREGGWARVCPKCGHE-HFPRIDP 145 (279)
T ss_pred cCCCCCCCcCccccCceeeeCCCCCCc-cCCCCCC
Confidence 358888888777666777789999654 6666655
No 69
>PHA00689 hypothetical protein
Probab=40.06 E-value=11 Score=21.38 Aligned_cols=11 Identities=36% Similarity=0.757 Sum_probs=8.9
Q ss_pred ccccccCCCCc
Q 036141 189 KFCNYCKKPGH 199 (220)
Q Consensus 189 ~~C~~Cgk~GH 199 (220)
..|-.|||.|-
T Consensus 18 vtckrcgktgl 28 (62)
T PHA00689 18 VTCKRCGKTGL 28 (62)
T ss_pred eehhhccccCc
Confidence 47999999874
No 70
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=39.32 E-value=18 Score=30.78 Aligned_cols=34 Identities=12% Similarity=0.099 Sum_probs=25.3
Q ss_pred CcccccCCCCCcccccccCccccccCCCCcccCCC
Q 036141 170 QVQCFSCKEYRHIVVKCAKKFCNYCKKPGHIIKEC 204 (220)
Q Consensus 170 ~~~~~~~~~~g~~~~~~~~~~C~~Cgk~GH~~~~C 204 (220)
++.|..||.+-.+..+. .-+|-.||..--....+
T Consensus 350 ~p~Cp~Cg~~m~S~G~~-g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 350 NPVCPRCGGRMKSAGRN-GFRCKKCGTRARETLIK 383 (421)
T ss_pred CCCCCccCCchhhcCCC-CcccccccccCCccccc
Confidence 67899999988876655 66899998765554444
No 71
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=39.00 E-value=13 Score=21.93 Aligned_cols=23 Identities=35% Similarity=0.862 Sum_probs=8.8
Q ss_pred cccCc---cccccCC---CCcccCCCCCC
Q 036141 185 KCAKK---FCNYCKK---PGHIIKECPTR 207 (220)
Q Consensus 185 ~~~~~---~C~~Cgk---~GH~~~~C~~k 207 (220)
.|+.. .|-.||- ..|+.+.||.+
T Consensus 27 ~CPvLr~y~Cp~CgAtGd~AHT~~yCP~k 55 (55)
T PF05741_consen 27 TCPVLRKYVCPICGATGDNAHTIKYCPKK 55 (55)
T ss_dssp --TTGGG---TTT---GGG---GGG-TT-
T ss_pred eCHHHhcCcCCCCcCcCccccccccCcCC
Confidence 45543 6888866 56888999864
No 72
>smart00400 ZnF_CHCC zinc finger.
Probab=39.00 E-value=23 Score=20.54 Aligned_cols=11 Identities=27% Similarity=0.715 Sum_probs=8.3
Q ss_pred cccccCCCCcc
Q 036141 190 FCNYCKKPGHI 200 (220)
Q Consensus 190 ~C~~Cgk~GH~ 200 (220)
.||.||+.|-.
T Consensus 25 ~Cf~cg~gGd~ 35 (55)
T smart00400 25 HCFGCGAGGNV 35 (55)
T ss_pred EEeCCCCCCCH
Confidence 68999887743
No 73
>TIGR02606 antidote_CC2985 putative addiction module antidote protein, CC2985 family. This bacterial protein family has a very similar seed alignment to that of Pfam model pfam03693 but is a more stringent model with higher cutoff scores. Proteins that score above the trusted cutoff to this model almost invariably are found adjacent to a ParE family protein (pfam05016), where ParE is the killing partner of an addiction module for plasmid stabilization. Members of this family, therefore, are putative addiction module antidote proteins. Some are encoded on plasmids or in prophage regions, but others appear chromosomal. A genome may contain several identical copies, such as the four in Magnetococcus sp. MC-1. This family is named for one member, CC2985 of Caulobacter crescentus CB15.
Probab=38.91 E-value=84 Score=19.32 Aligned_cols=36 Identities=14% Similarity=0.065 Sum_probs=28.1
Q ss_pred hhccchHHHHHHhhcCCCCCCCHHHHHHHHHHHHHH
Q 036141 102 MKLRPKYEAARSNLMNRDLSPSLDVCFKELLREEQR 137 (220)
Q Consensus 102 ~gLp~~~~~~~~~l~~~~~~~sl~e~~~~l~~~e~~ 137 (220)
..||+.+..++......-.+.+..|++..+++....
T Consensus 4 isL~~~~~~~i~~~V~sG~Y~s~SEVir~aLR~le~ 39 (69)
T TIGR02606 4 VSLGEHLESFIRSQVQSGRYGSASEVVRAALRLLEE 39 (69)
T ss_pred eecCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHH
Confidence 367888999988888877788888888887765443
No 74
>PF13376 OmdA: Bacteriocin-protection, YdeI or OmpD-Associated
Probab=37.24 E-value=92 Score=18.57 Aligned_cols=28 Identities=25% Similarity=0.417 Sum_probs=23.2
Q ss_pred cchHHHHhhccccccHHHHHHHHHHHhc
Q 036141 7 SIDQSLILNLKLHKTAKDMWEYLKKVYN 34 (220)
Q Consensus 7 sl~~~~~~~~~~~~ta~~~w~~L~~~f~ 34 (220)
-|.+++...+...+.|.+.|..|-..|.
T Consensus 5 ~vP~dl~~aL~~~p~a~~~f~~l~~~~r 32 (63)
T PF13376_consen 5 EVPEDLEAALEANPEAKEFFESLTPSYR 32 (63)
T ss_pred CCCHHHHHHHHCCHHHHHHHHHCCHHHH
Confidence 3678888899999999999998887664
No 75
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=36.84 E-value=14 Score=22.17 Aligned_cols=8 Identities=38% Similarity=0.629 Sum_probs=6.5
Q ss_pred cccccCCC
Q 036141 190 FCNYCKKP 197 (220)
Q Consensus 190 ~C~~Cgk~ 197 (220)
.||-||++
T Consensus 6 RCFsCGkv 13 (63)
T COG1644 6 RCFSCGKV 13 (63)
T ss_pred EeecCCCC
Confidence 59999885
No 76
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=36.48 E-value=32 Score=24.25 Aligned_cols=32 Identities=13% Similarity=0.384 Sum_probs=21.4
Q ss_pred ccccCCCCCcccccc-cC-ccccccCCCCcccCC
Q 036141 172 QCFSCKEYRHIVVKC-AK-KFCNYCKKPGHIIKE 203 (220)
Q Consensus 172 ~~~~~~~~g~~~~~~-~~-~~C~~Cgk~GH~~~~ 203 (220)
.|+.|+......... .. -.|.+|+...++-.+
T Consensus 2 ~C~fC~~~s~~~~~~~~~~w~C~~C~q~N~f~e~ 35 (131)
T PF09779_consen 2 NCWFCGQNSKVPYDNRNSNWTCPHCEQYNGFDED 35 (131)
T ss_pred eeccCCCCCCCCCCCCCCeeECCCCCCccCcccc
Confidence 589998887664432 22 479999877666544
No 77
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=36.39 E-value=18 Score=21.62 Aligned_cols=10 Identities=50% Similarity=1.145 Sum_probs=7.5
Q ss_pred CccccccCCC
Q 036141 188 KKFCNYCKKP 197 (220)
Q Consensus 188 ~~~C~~Cgk~ 197 (220)
.+.|.+||++
T Consensus 3 HkHC~~CG~~ 12 (59)
T PF09889_consen 3 HKHCPVCGKP 12 (59)
T ss_pred CCcCCcCCCc
Confidence 3469999876
No 78
>PF15629 Perm-CXXC: Permuted single zf-CXXC unit
Probab=36.32 E-value=25 Score=18.10 Aligned_cols=12 Identities=25% Similarity=0.783 Sum_probs=9.8
Q ss_pred cccCccccccCC
Q 036141 185 KCAKKFCNYCKK 196 (220)
Q Consensus 185 ~~~~~~C~~Cgk 196 (220)
-|....||.|+.
T Consensus 13 LC~~~tCfsCNs 24 (32)
T PF15629_consen 13 LCDEETCFSCNS 24 (32)
T ss_pred ccCCcccccccc
Confidence 588889999975
No 79
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=36.24 E-value=14 Score=24.49 Aligned_cols=12 Identities=33% Similarity=0.553 Sum_probs=6.9
Q ss_pred ccccccCCCCcc
Q 036141 189 KFCNYCKKPGHI 200 (220)
Q Consensus 189 ~~C~~Cgk~GH~ 200 (220)
-+||.||+.|-.
T Consensus 55 ~~Cf~Cg~~Gd~ 66 (97)
T PF01807_consen 55 FKCFGCGKGGDV 66 (97)
T ss_dssp EEETTT--EE-H
T ss_pred EEECCCCCCCcH
Confidence 379999988743
No 80
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=35.65 E-value=19 Score=31.16 Aligned_cols=20 Identities=35% Similarity=0.845 Sum_probs=18.2
Q ss_pred ccccccCCCCcccCCCCCCC
Q 036141 189 KFCNYCKKPGHIIKECPTRP 208 (220)
Q Consensus 189 ~~C~~Cgk~GH~~~~C~~k~ 208 (220)
..|..||..||..-+||.+-
T Consensus 262 ~~c~~cg~~~H~q~~cp~r~ 281 (554)
T KOG0119|consen 262 RACRNCGSTGHKQYDCPGRI 281 (554)
T ss_pred ccccccCCCccccccCCccc
Confidence 47999999999999999883
No 81
>PF06757 Ins_allergen_rp: Insect allergen related repeat, nitrile-specifier detoxification; InterPro: IPR010629 This entry represents several insect specific allergen repeats. These repeats are commonly found in various proteins from cockroaches, fruit flies and mosquitos. It has been suggested that the repeat sequences have evolved by duplication of an ancestral amino acid domain, which may have arisen from the mitochondrial energy transfer proteins []. This family exemplifies a case of novel gene evolution. The case in point is the arms-race between plants and their infective insective herbivores in the area of the glucosinolate-myrosinase system. Brassicas have developed the glucosinolate-myrosinase system as chemical defence mechanism against the insects, and consequently the insects have adapted to produce a detoxifying molecule, nitrile-specifier protein (NSP). NSP is present in the Pieris rapae (Cabbage white butterfly). NSP is structurally different from and has no amino acid homology to any known detoxifying enzymes, and it appears to have arisen by a process of domain and gene duplication of a sequence of unknown function that is widespread in insect species and referred to as insect-allergen-repeat protein. Thus this family is found either as a single domain or as a multiple repeat-domain [].
Probab=35.47 E-value=1.8e+02 Score=21.49 Aligned_cols=80 Identities=14% Similarity=0.051 Sum_probs=41.0
Q ss_pred HHHhcCCccHHHHHHHHHHHHHHHhhcccccCCcc-cHHHHHHHHHHHHHHHHHhhccchHHHHHHhhcC-CCCCCCHHH
Q 036141 49 ARYSQGNLSIQNYFSGFQNLWAEYVDMIYVQVPIE-SLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMN-RDLSPSLDV 126 (220)
Q Consensus 49 ~~~~q~~~sv~~y~~~~~~l~~~L~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~gLp~~~~~~~~~l~~-~~~~~sl~e 126 (220)
..+...|-+|..|++.+..+. .+..+.+...... ... .-...+..++.-||-+ .++.-+.. ......|.+
T Consensus 64 ~yL~~~gldv~~~i~~i~~~l-~~~~~~p~~~~~~~~~~-----g~~g~~~di~~~lP~~--~l~aL~~~K~~~s~~F~~ 135 (179)
T PF06757_consen 64 DYLESAGLDVYYYINQINDLL-GLPPLNPTPSLSCSRGG-----GLNGFVDDILALLPRD--KLRALYEEKLATSPEFAE 135 (179)
T ss_pred HHHHHCCCCHHHHHHHHHHHH-cCCcCCCCcccccccCC-----CHHHHHHHHHHHCCHH--HHHHHHHHHHHCCHHHHH
Confidence 344456889999999999885 3332211111000 011 1234455567777743 22222211 122345777
Q ss_pred HHHHHHHHHH
Q 036141 127 CFKELLREEQ 136 (220)
Q Consensus 127 ~~~~l~~~e~ 136 (220)
+++.+.+.|-
T Consensus 136 f~~~l~S~ef 145 (179)
T PF06757_consen 136 FVEALRSPEF 145 (179)
T ss_pred HHHHHcCHHH
Confidence 7887777753
No 82
>PF03693 RHH_2: Uncharacterised protein family (UPF0156); InterPro: IPR022789 This family of proteins are about 80 amino acids in length and their function is unknown. The proteins contain a conserved GRY motif. This family appears to be related to ribbon-helix-helix DNA-binding proteins. ; PDB: 3KXE_C.
Probab=35.43 E-value=1.2e+02 Score=19.31 Aligned_cols=32 Identities=25% Similarity=0.283 Sum_probs=23.9
Q ss_pred hhccchHHHHHHhhcCCCCCCCHHHHHHHHHH
Q 036141 102 MKLRPKYEAARSNLMNRDLSPSLDVCFKELLR 133 (220)
Q Consensus 102 ~gLp~~~~~~~~~l~~~~~~~sl~e~~~~l~~ 133 (220)
..||+.++.++.....+-.+-|..|++..+++
T Consensus 7 isL~~~~~~~i~~~V~sG~Y~s~SEvvR~aLR 38 (80)
T PF03693_consen 7 ISLTPELEAFIEEQVASGRYSSASEVVREALR 38 (80)
T ss_dssp E---HHHHHHHHHHHCTTS-SSHHHHHHHHHH
T ss_pred EecCHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence 46899999999999888888999999877655
No 83
>PRK05772 translation initiation factor IF-2B subunit alpha; Provisional
Probab=34.94 E-value=2.8e+02 Score=23.43 Aligned_cols=64 Identities=6% Similarity=-0.116 Sum_probs=42.3
Q ss_pred ccccccHHHHHHHHHHHhccCChhH-HhHHHHH-HHHHhcCCccHHHHHHHHHHHHHHHhhccccc
Q 036141 16 LKLHKTAKDMWEYLKKVYNQDNTAK-RSHLEYE-IARYSQGNLSIQNYFSGFQNLWAEYVDMIYVQ 79 (220)
Q Consensus 16 ~~~~~ta~~~w~~L~~~f~~~~~~~-~~~l~~~-~~~~~q~~~sv~~y~~~~~~l~~~L~~~~~~~ 79 (220)
+..+.+..++|..++++=-....+- +....-- +......+.++.+|...+....+.|....+..
T Consensus 40 ~~~~~~~~~v~~aI~~M~vRGApaigiaAa~glal~~~~~~~~~~~~~~~~l~~~~~~L~~aRPTa 105 (363)
T PRK05772 40 YVDLKTVEEVALAIRNMQVRGAPAIGITAGYGMVLALIENNVKTLDDAIRELTRAKTILDSARPTA 105 (363)
T ss_pred EEEeCCHHHHHHHHHhCcccCCcHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHhcCCcH
Confidence 4457899999999999887655543 1111111 22222235589999999999999997665443
No 84
>COG5420 Uncharacterized conserved small protein containing a coiled-coil domain [Function unknown]
Probab=34.25 E-value=59 Score=19.67 Aligned_cols=14 Identities=14% Similarity=0.117 Sum_probs=11.4
Q ss_pred HHhhccchHHHHHH
Q 036141 100 FLMKLRPKYEAARS 113 (220)
Q Consensus 100 ~l~gLp~~~~~~~~ 113 (220)
+-.|||..|..+-.
T Consensus 32 LAEgLP~~wtei~~ 45 (71)
T COG5420 32 LAEGLPVKWTEIMA 45 (71)
T ss_pred HhccCCccHHHHHH
Confidence 88999999988743
No 85
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=33.73 E-value=81 Score=20.70 Aligned_cols=25 Identities=24% Similarity=0.163 Sum_probs=14.7
Q ss_pred HHHHhhcCCCCCCCHHHHHHHHHHH
Q 036141 110 AARSNLMNRDLSPSLDVCFKELLRE 134 (220)
Q Consensus 110 ~~~~~l~~~~~~~sl~e~~~~l~~~ 134 (220)
.++..|+.++...++.++...+..+
T Consensus 7 kii~lL~e~~eplt~~ei~~~~~~~ 31 (97)
T COG3357 7 KIISLLLESDEPLTVAEIFELLNGE 31 (97)
T ss_pred HHHHHHHcCCCcchHHHHHHHHcCC
Confidence 3444455556666777777666443
No 86
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=33.56 E-value=17 Score=19.88 Aligned_cols=11 Identities=36% Similarity=1.126 Sum_probs=5.0
Q ss_pred ccccccCCCCc
Q 036141 189 KFCNYCKKPGH 199 (220)
Q Consensus 189 ~~C~~Cgk~GH 199 (220)
..|.+||++.-
T Consensus 2 ~~CSFCgr~~~ 12 (41)
T PF06689_consen 2 KRCSFCGRPES 12 (41)
T ss_dssp -B-TTT--BTT
T ss_pred CCccCCCCCHH
Confidence 36999998753
No 87
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=33.35 E-value=16 Score=21.84 Aligned_cols=8 Identities=38% Similarity=0.630 Sum_probs=6.5
Q ss_pred cccccCCC
Q 036141 190 FCNYCKKP 197 (220)
Q Consensus 190 ~C~~Cgk~ 197 (220)
.||.|||.
T Consensus 6 RCFtCGKv 13 (69)
T KOG3497|consen 6 RCFTCGKV 13 (69)
T ss_pred Eeeecccc
Confidence 59999985
No 88
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=33.10 E-value=25 Score=19.61 Aligned_cols=25 Identities=20% Similarity=0.303 Sum_probs=14.0
Q ss_pred ccccCCCCCcccccccCccccccCCC
Q 036141 172 QCFSCKEYRHIVVKCAKKFCNYCKKP 197 (220)
Q Consensus 172 ~~~~~~~~g~~~~~~~~~~C~~Cgk~ 197 (220)
.|..||..-... ......|.+||..
T Consensus 4 ~C~~Cg~~~~~~-~~~~irC~~CG~r 28 (44)
T smart00659 4 ICGECGRENEIK-SKDVVRCRECGYR 28 (44)
T ss_pred ECCCCCCEeecC-CCCceECCCCCce
Confidence 366666654432 2344578888653
No 89
>KOG4451 consensus Uncharacterized conserved protein (tumor-associated antigen HCA127 in humans) [Function unknown]
Probab=33.02 E-value=57 Score=25.35 Aligned_cols=18 Identities=33% Similarity=0.669 Sum_probs=11.8
Q ss_pred ccccccCCCCcc-cCCCCC
Q 036141 189 KFCNYCKKPGHI-IKECPT 206 (220)
Q Consensus 189 ~~C~~Cgk~GH~-~~~C~~ 206 (220)
+.|-.||.-=|. +-.||.
T Consensus 250 K~ClsChqqIHRNAPiCPl 268 (286)
T KOG4451|consen 250 KVCLSCHQQIHRNAPICPL 268 (286)
T ss_pred hHHHHHHHHHhcCCCCCcc
Confidence 368888877775 345664
No 90
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=32.75 E-value=20 Score=21.08 Aligned_cols=17 Identities=24% Similarity=0.765 Sum_probs=10.2
Q ss_pred cccccCCCCccc----CCCCC
Q 036141 190 FCNYCKKPGHII----KECPT 206 (220)
Q Consensus 190 ~C~~Cgk~GH~~----~~C~~ 206 (220)
-|++||..=--. +.||=
T Consensus 29 YC~~Cg~~Y~d~~dL~~~CPG 49 (55)
T PF13821_consen 29 YCFWCGTKYDDEEDLERNCPG 49 (55)
T ss_pred eeeeeCCccCCHHHHHhCCCC
Confidence 588887654433 45653
No 91
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=32.67 E-value=20 Score=21.56 Aligned_cols=8 Identities=38% Similarity=0.630 Sum_probs=5.6
Q ss_pred cccccCCC
Q 036141 190 FCNYCKKP 197 (220)
Q Consensus 190 ~C~~Cgk~ 197 (220)
.||-||+.
T Consensus 6 RCFTCGkv 13 (60)
T PF01194_consen 6 RCFTCGKV 13 (60)
T ss_dssp S-STTTSB
T ss_pred ecCCCCCC
Confidence 59999885
No 92
>PF14353 CpXC: CpXC protein
Probab=32.63 E-value=21 Score=24.88 Aligned_cols=15 Identities=13% Similarity=0.186 Sum_probs=12.8
Q ss_pred cccccCCCCcccCCC
Q 036141 190 FCNYCKKPGHIIKEC 204 (220)
Q Consensus 190 ~C~~Cgk~GH~~~~C 204 (220)
.|.+||+.++....|
T Consensus 40 ~CP~Cg~~~~~~~p~ 54 (128)
T PF14353_consen 40 TCPSCGHKFRLEYPL 54 (128)
T ss_pred ECCCCCCceecCCCE
Confidence 799999999887665
No 93
>PF14567 SUKH_5: SMI1-KNR4 cell-wall; PDB: 2PAG_A.
Probab=32.22 E-value=97 Score=21.94 Aligned_cols=18 Identities=17% Similarity=0.215 Sum_probs=10.3
Q ss_pred HHHHhhccchHHHHHHhh
Q 036141 98 DQFLMKLRPKYEAARSNL 115 (220)
Q Consensus 98 ~~~l~gLp~~~~~~~~~l 115 (220)
.++...||++|+.+....
T Consensus 32 e~L~i~lP~eyk~fL~~~ 49 (132)
T PF14567_consen 32 EQLGISLPEEYKEFLLEA 49 (132)
T ss_dssp HHHT----HHHHHHHHHH
T ss_pred HHHCCCCCHHHHHHHHHC
Confidence 348889999999887643
No 94
>cd07936 SCAN SCAN oligomerization domain. The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several vertebrate proteins that contain C2H2 zinc finger motifs, many of which may be transcription factors playing roles in cell survival and differentiation. This protein-interaction domain is able to mediate homo- and hetero-oligomerization of SCAN-containing proteins. Some SCAN-containing proteins, including those of lower vertebrates, do not contain zinc finger motifs. It has been noted that the SCAN domain resembles a domain-swapped version of the C-terminal domain of the HIV capsid protein. This domain model features elements common to the three general groups of SCAN domains (SCAN-A1, SCAN-A2, and SCAN-B). The SCAND1 protein is truncated at the C-terminus with respect to this model, the SCAND2 protein appears to have a truncated central helix.
Probab=32.12 E-value=1.4e+02 Score=19.19 Aligned_cols=75 Identities=13% Similarity=0.100 Sum_probs=45.6
Q ss_pred HHHHHHHh-cCCccHHHHHHHHHHHHHHHhhcccccCCcccHHHHHHHHHHHHHHHHHhhccchHHHHHHhhcCCCCCCC
Q 036141 45 EYEIARYS-QGNLSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRDLSPS 123 (220)
Q Consensus 45 ~~~~~~~~-q~~~sv~~y~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~gLp~~~~~~~~~l~~~~~~~s 123 (220)
+..|.... +++.+..+++.+++.|+.+=- .+... .-..+.+..-..+|+.-||+++..-+. . ...-|
T Consensus 5 r~~FR~f~~~~~~~p~eal~~L~eLc~~WL--rpe~~------tkeqilelLVlEQfl~~lp~e~q~~v~---~-~~p~s 72 (85)
T cd07936 5 RQRFRAFQYQEASGPREALQRLRELCRQWL--RPEIH------TKEQILELLVLEQFLIILPPEVQAWVR---E-RKPES 72 (85)
T ss_pred HHHHhccccCCCCChHHHHHHHHHHHHHHc--chhhc------CHHHHHHHHHHHHHhhhCCHHHHHHHH---h-cCCCC
Confidence 34466655 578899999999999977653 11111 112235555668899999997655422 2 23345
Q ss_pred HHHHHHHH
Q 036141 124 LDVCFKEL 131 (220)
Q Consensus 124 l~e~~~~l 131 (220)
-++++..+
T Consensus 73 ~eea~~l~ 80 (85)
T cd07936 73 GEEAATLA 80 (85)
T ss_pred HHHHHHHH
Confidence 56665544
No 95
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=32.11 E-value=99 Score=20.98 Aligned_cols=32 Identities=19% Similarity=0.049 Sum_probs=20.3
Q ss_pred ccccccHHHHHHHHHHHhccCChhHHhHHHHH
Q 036141 16 LKLHKTAKDMWEYLKKVYNQDNTAKRSHLEYE 47 (220)
Q Consensus 16 ~~~~~ta~~~w~~L~~~f~~~~~~~~~~l~~~ 47 (220)
....-||.++|+.|+.....-+.+.+++.-..
T Consensus 20 ~~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~ 51 (120)
T PF01475_consen 20 SPEHLTAEEIYDKLRKKGPRISLATVYRTLDL 51 (120)
T ss_dssp HSSSEEHHHHHHHHHHTTTT--HHHHHHHHHH
T ss_pred CCCCCCHHHHHHHhhhccCCcCHHHHHHHHHH
Confidence 33477999999999976665556655544333
No 96
>KOG4204 consensus Histone deacetylase complex, SIN3 component [Chromatin structure and dynamics]
Probab=31.71 E-value=1.3e+02 Score=23.49 Aligned_cols=53 Identities=17% Similarity=0.213 Sum_probs=37.1
Q ss_pred cccccHHHHHHHHHHHhccCChhHHhHHHHHHHHHhcCCccHHHHHHHHHHHHH
Q 036141 17 KLHKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQGNLSIQNYFSGFQNLWA 70 (220)
Q Consensus 17 ~~~~ta~~~w~~L~~~f~~~~~~~~~~l~~~~~~~~q~~~sv~~y~~~~~~l~~ 70 (220)
..+.-+..+.+.++.+|.... .-+.....-+...+.+..++.+...++..|+.
T Consensus 125 ~~~~~a~~fv~klk~rf~~~~-~v~~s~l~il~~y~~~~ks~~e~~~eV~~L~~ 177 (231)
T KOG4204|consen 125 VEFDRAISFVNKLKTRFQGDD-HVYKSFLEILRMYQEGNKSVSEVYQEVEALLQ 177 (231)
T ss_pred chHHHHHHHHHHHHHHhcCCH-HHHHHHHHHHHHHhhccchHHHHHHHHHHHHc
Confidence 345567789999999998655 22233333366667788999998888887754
No 97
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=31.67 E-value=31 Score=19.04 Aligned_cols=12 Identities=33% Similarity=0.924 Sum_probs=8.6
Q ss_pred ccCccccccCCC
Q 036141 186 CAKKFCNYCKKP 197 (220)
Q Consensus 186 ~~~~~C~~Cgk~ 197 (220)
-+.+.|-.||.+
T Consensus 6 lp~K~C~~C~rp 17 (42)
T PF10013_consen 6 LPSKICPVCGRP 17 (42)
T ss_pred CCCCcCcccCCc
Confidence 455678888876
No 98
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=31.56 E-value=24 Score=20.27 Aligned_cols=24 Identities=21% Similarity=0.508 Sum_probs=13.4
Q ss_pred cccCCCCCcccccccCccccccCC
Q 036141 173 CFSCKEYRHIVVKCAKKFCNYCKK 196 (220)
Q Consensus 173 ~~~~~~~g~~~~~~~~~~C~~Cgk 196 (220)
|..|+..-..-.......|.+||.
T Consensus 9 C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 9 CARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred hhhcCCeeehhhccCceeCCCCCc
Confidence 566666543222344457888874
No 99
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=31.45 E-value=28 Score=18.08 Aligned_cols=25 Identities=16% Similarity=0.477 Sum_probs=15.1
Q ss_pred ccccCCCCCcccccccCccccccCC
Q 036141 172 QCFSCKEYRHIVVKCAKKFCNYCKK 196 (220)
Q Consensus 172 ~~~~~~~~g~~~~~~~~~~C~~Cgk 196 (220)
.|..|+..+=..++.....|-.||.
T Consensus 5 ~C~~C~~~~i~~~~~~~~~C~~Cg~ 29 (33)
T PF08792_consen 5 KCSKCGGNGIVNKEDDYEVCIFCGS 29 (33)
T ss_pred EcCCCCCCeEEEecCCeEEcccCCc
Confidence 4666666665544555556777764
No 100
>KOG2203 consensus GTP-binding protein [General function prediction only]
Probab=31.35 E-value=1.3e+02 Score=27.12 Aligned_cols=52 Identities=8% Similarity=0.265 Sum_probs=38.8
Q ss_pred cHHHHHHHHHHHhccCChhHHhHHHHHHHHHh--cCCccHHHHHHHHHHHHHHH
Q 036141 21 TAKDMWEYLKKVYNQDNTAKRSHLEYEIARYS--QGNLSIQNYFSGFQNLWAEY 72 (220)
Q Consensus 21 ta~~~w~~L~~~f~~~~~~~~~~l~~~~~~~~--q~~~sv~~y~~~~~~l~~~L 72 (220)
-.+++|..+++.|.......++.+.....-.. .+.++.++|+..|+.+...+
T Consensus 479 ~s~evW~ti~n~f~~e~n~av~~~~~~~~~f~~~~de~t~~~m~~nlk~~a~~~ 532 (772)
T KOG2203|consen 479 ASKEVWDTIRNLFRRETNTAVYGLSNAVYGFEIGLDEETRDKMVKNLKNYAWGT 532 (772)
T ss_pred cccccHHHHHHHHHhccchhHHHHhhcccccccccchhhHHHHHHHHHHHHHHH
Confidence 34789999999999766666677666655555 45788899999988775554
No 101
>PF13395 HNH_4: HNH endonuclease
Probab=31.11 E-value=22 Score=20.67 Aligned_cols=7 Identities=71% Similarity=1.882 Sum_probs=5.4
Q ss_pred ccccCCC
Q 036141 191 CNYCKKP 197 (220)
Q Consensus 191 C~~Cgk~ 197 (220)
|+|||++
T Consensus 1 C~Y~g~~ 7 (54)
T PF13395_consen 1 CPYCGKP 7 (54)
T ss_pred CCCCCCC
Confidence 7888875
No 102
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=30.85 E-value=32 Score=27.45 Aligned_cols=31 Identities=23% Similarity=0.351 Sum_probs=18.0
Q ss_pred CcccccCCCCCcccccccCc----cccccCCCCcc
Q 036141 170 QVQCFSCKEYRHIVVKCAKK----FCNYCKKPGHI 200 (220)
Q Consensus 170 ~~~~~~~~~~g~~~~~~~~~----~C~~Cgk~GH~ 200 (220)
++-|.+|-+-.+-+++...+ -|.-||+.||-
T Consensus 224 n~YCDFclgdsr~nkkt~~peelvscsdcgrsghp 258 (336)
T KOG1244|consen 224 NPYCDFCLGDSRENKKTGMPEELVSCSDCGRSGHP 258 (336)
T ss_pred CcccceeccccccccccCCchhhcchhhcCCCCCc
Confidence 45577776554443332222 58888888884
No 103
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=30.68 E-value=22 Score=23.10 Aligned_cols=9 Identities=33% Similarity=0.637 Sum_probs=6.9
Q ss_pred cccccCCCC
Q 036141 190 FCNYCKKPG 198 (220)
Q Consensus 190 ~C~~Cgk~G 198 (220)
.|+|||.+=
T Consensus 2 ~C~HCg~~~ 10 (88)
T PF12156_consen 2 KCYHCGLPV 10 (88)
T ss_pred CCCCCCCCC
Confidence 599998764
No 104
>KOG2985 consensus Uncharacterized conserved protein [Function unknown]
Probab=30.36 E-value=13 Score=29.10 Aligned_cols=18 Identities=28% Similarity=0.781 Sum_probs=15.8
Q ss_pred ccccccCCCCcccCCCCC
Q 036141 189 KFCNYCKKPGHIIKECPT 206 (220)
Q Consensus 189 ~~C~~Cgk~GH~~~~C~~ 206 (220)
+-|-.||.+||..-+|++
T Consensus 82 g~ckRcg~~ghl~fqcRn 99 (306)
T KOG2985|consen 82 GSCKRCGRVGHLTFQCRN 99 (306)
T ss_pred cchhhccccchhhHHHhh
Confidence 459999999999999975
No 105
>KOG2344 consensus Exocyst component protein and related proteins [Intracellular trafficking, secretion, and vesicular transport]
Probab=30.32 E-value=1.8e+02 Score=26.58 Aligned_cols=100 Identities=12% Similarity=0.183 Sum_probs=64.3
Q ss_pred chHHHHhhccccccHHHHHHHHHHHhccCChhHHhHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHhhcccccCCcccHH
Q 036141 8 IDQSLILNLKLHKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQG-NLSIQNYFSGFQNLWAEYVDMIYVQVPIESLA 86 (220)
Q Consensus 8 l~~~~~~~~~~~~ta~~~w~~L~~~f~~~~~~~~~~l~~~~~~~~q~-~~sv~~y~~~~~~l~~~L~~~~~~~~~~~~~~ 86 (220)
-..+++..+.-+++..++|-.+...|.....+ .++.++...... ++.+...+.+|...+..=.+ ..++|+..+.
T Consensus 313 ~pEklf~iLd~y~~i~~l~p~ie~lF~~~~~s---~vr~~~~~~~~rL~~~~~~~~~efe~~I~~d~s--k~pv~gG~VH 387 (623)
T KOG2344|consen 313 SPEKLFKLLDLYETIVELRPDIERLFSDASCS---EVRSQALSLLKRLGEGVRSIFVEFESAIRKDSS--KTPVPGGGVH 387 (623)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhccCccCH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC--CCCCCCCCcC
Confidence 35677777888899999999999999854432 234444444332 56777788777766544332 4555665443
Q ss_pred HHHHHHHHHHHHHHHhhccchHHHHHHhhcCC
Q 036141 87 DVQEVHEQSKRDQFLMKLRPKYEAARSNLMNR 118 (220)
Q Consensus 87 ~~~~~~~~~~~~~~l~gLp~~~~~~~~~l~~~ 118 (220)
-+ +.=++.++.-|. +|.....+++..
T Consensus 388 pL-----Tryvmnyl~~L~-dy~~tL~~il~~ 413 (623)
T KOG2344|consen 388 PL-----TRYVMNYLNFLA-DYKDTLEQLLME 413 (623)
T ss_pred hh-----HHHHHHHHHHHH-HHHHHHHHHHhc
Confidence 33 333566777777 677777777664
No 106
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=30.20 E-value=23 Score=20.81 Aligned_cols=19 Identities=37% Similarity=0.882 Sum_probs=14.0
Q ss_pred ccCccccccCCCCcccCCC
Q 036141 186 CAKKFCNYCKKPGHIIKEC 204 (220)
Q Consensus 186 ~~~~~C~~Cgk~GH~~~~C 204 (220)
|....|+.|+.+-|.-..|
T Consensus 46 C~~~fC~~C~~~~H~~~~C 64 (64)
T PF01485_consen 46 CGTEFCFKCGEPWHEGVTC 64 (64)
T ss_dssp CCSEECSSSTSESCTTS-H
T ss_pred CCCcCccccCcccCCCCCC
Confidence 5556899999999976554
No 107
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=30.14 E-value=29 Score=23.70 Aligned_cols=25 Identities=20% Similarity=0.719 Sum_probs=17.3
Q ss_pred ccccCCCCCcccccccCccccccCC
Q 036141 172 QCFSCKEYRHIVVKCAKKFCNYCKK 196 (220)
Q Consensus 172 ~~~~~~~~g~~~~~~~~~~C~~Cgk 196 (220)
.|..|+...-....|.+..|..||.
T Consensus 44 ~C~~Cg~~~~~~~SCk~R~CP~C~~ 68 (111)
T PF14319_consen 44 RCEDCGHEKIVYNSCKNRHCPSCQA 68 (111)
T ss_pred ecCCCCceEEecCcccCcCCCCCCC
Confidence 4777777666666677777777764
No 108
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=29.86 E-value=15 Score=21.40 Aligned_cols=12 Identities=25% Similarity=0.520 Sum_probs=7.2
Q ss_pred CCcccCCCCCCC
Q 036141 197 PGHIIKECPTRP 208 (220)
Q Consensus 197 ~GH~~~~C~~k~ 208 (220)
.||....||.-+
T Consensus 20 ~~yle~KCPrCK 31 (60)
T COG4416 20 QAYLEKKCPRCK 31 (60)
T ss_pred ceeeeecCCccc
Confidence 466666676543
No 109
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=29.85 E-value=23 Score=22.02 Aligned_cols=8 Identities=38% Similarity=0.630 Sum_probs=6.6
Q ss_pred cccccCCC
Q 036141 190 FCNYCKKP 197 (220)
Q Consensus 190 ~C~~Cgk~ 197 (220)
.||-|||.
T Consensus 6 RCFTCGkv 13 (71)
T PLN00032 6 RCFTCGKV 13 (71)
T ss_pred eecCCCCC
Confidence 59999985
No 110
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=29.49 E-value=23 Score=21.38 Aligned_cols=8 Identities=38% Similarity=0.630 Sum_probs=6.6
Q ss_pred cccccCCC
Q 036141 190 FCNYCKKP 197 (220)
Q Consensus 190 ~C~~Cgk~ 197 (220)
.||-|||.
T Consensus 6 RCFTCGkv 13 (62)
T PRK04016 6 RCFTCGKV 13 (62)
T ss_pred EecCCCCC
Confidence 59999985
No 111
>PF05515 Viral_NABP: Viral nucleic acid binding ; InterPro: IPR008891 This family is common to ssRNA positive-strand viruses and are commonly described as nucleic acid binding proteins (NABP).
Probab=29.15 E-value=90 Score=21.81 Aligned_cols=20 Identities=20% Similarity=0.343 Sum_probs=15.9
Q ss_pred ccccccCCCCcccCCCCCCC
Q 036141 189 KFCNYCKKPGHIIKECPTRP 208 (220)
Q Consensus 189 ~~C~~Cgk~GH~~~~C~~k~ 208 (220)
..|+.||+.-|.-..|+...
T Consensus 63 ~~C~~CG~~l~~~~~C~~~~ 82 (124)
T PF05515_consen 63 NRCFKCGRYLHNNGNCRRNT 82 (124)
T ss_pred CccccccceeecCCcCCCcc
Confidence 46999999888888898433
No 112
>smart00431 SCAN leucine rich region.
Probab=28.75 E-value=2e+02 Score=19.79 Aligned_cols=78 Identities=14% Similarity=0.079 Sum_probs=48.0
Q ss_pred HHHHHHHh-cCCccHHHHHHHHHHHHHHHhhcccccCCcccHHHHHHHHHHHHHHHHHhhccchHHHHHHhhcCCCCCCC
Q 036141 45 EYEIARYS-QGNLSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRDLSPS 123 (220)
Q Consensus 45 ~~~~~~~~-q~~~sv~~y~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~gLp~~~~~~~~~l~~~~~~~s 123 (220)
+..|.+.. ++.....+++.+++.|+..=- .+...+ -..+.+.....+||.-||.++..-+. ....-|
T Consensus 5 r~~FR~f~y~e~~gp~eaL~~L~eLc~~WL--rPe~~t------KeqilElLVlEQFL~ilP~e~q~wv~----~~~p~s 72 (113)
T smart00431 5 RQRFRQFRYQETSGPREALSRLRELCRQWL--RPELHT------KEQILELLVLEQFLTILPGELQAWVR----EHHPES 72 (113)
T ss_pred HHHhhccccCCCCChHHHHHHHHHHHHhhc--Chhhhh------HHHHHHHHHHHHHhccCcHHHHHHHH----hcCCCC
Confidence 34465554 678889999999998876653 111111 11234555568899999998776522 233346
Q ss_pred HHHHHHHHHHH
Q 036141 124 LDVCFKELLRE 134 (220)
Q Consensus 124 l~e~~~~l~~~ 134 (220)
-++++..+...
T Consensus 73 geeav~l~E~l 83 (113)
T smart00431 73 GEEAVTLLEDL 83 (113)
T ss_pred HHHHHHHHHHh
Confidence 67776665544
No 113
>PF09580 Spore_YhcN_YlaJ: Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ); InterPro: IPR019076 This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain.
Probab=28.08 E-value=2.4e+02 Score=20.59 Aligned_cols=51 Identities=6% Similarity=0.037 Sum_probs=34.4
Q ss_pred HHHHHHHHHHhcc------CChhHHhHHHHHHHHHhcCCccHHHHHHHHHHHHHHHh
Q 036141 23 KDMWEYLKKVYNQ------DNTAKRSHLEYEIARYSQGNLSIQNYFSGFQNLWAEYV 73 (220)
Q Consensus 23 ~~~w~~L~~~f~~------~~~~~~~~l~~~~~~~~q~~~sv~~y~~~~~~l~~~L~ 73 (220)
+++-+.+++.+-. .+.+.++.-.+.|....+.++++.+|..+|..|+.+|.
T Consensus 120 ~~V~~~v~~~~p~~~~V~Vs~D~~~~~ri~~~~~~~~~g~~~~~~~~~~~~i~~r~~ 176 (177)
T PF09580_consen 120 KKVEKAVKSADPRIYNVYVSTDPDIFDRIRNLANRIRNGRPVSGFNDEIKEIVRRMF 176 (177)
T ss_pred HHHHHHHHHhCCCccEEEEEcCHHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHhhC
Confidence 4555556655432 34455555555577777778899999999999988774
No 114
>COG1940 NagC Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]
Probab=27.71 E-value=32 Score=27.87 Aligned_cols=31 Identities=23% Similarity=0.329 Sum_probs=22.0
Q ss_pred ccccCCCCCcccccccCccccccCCCCcccCCC
Q 036141 172 QCFSCKEYRHIVVKCAKKFCNYCKKPGHIIKEC 204 (220)
Q Consensus 172 ~~~~~~~~g~~~~~~~~~~C~~Cgk~GH~~~~C 204 (220)
.....+.-||..-..... | .||+.|++...+
T Consensus 158 ~~g~age~Gh~~v~~~g~-c-~cG~~GclE~~a 188 (314)
T COG1940 158 ANGNAGEIGHMVVDPDGE-C-GCGRRGCLETYA 188 (314)
T ss_pred CCCccccccceEECCCCc-c-CCCCCCchHHhc
Confidence 344556677876554444 9 999999988765
No 115
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=27.27 E-value=31 Score=24.66 Aligned_cols=23 Identities=17% Similarity=0.582 Sum_probs=14.1
Q ss_pred ccccCCCCCcccccccCccccccCCCC
Q 036141 172 QCFSCKEYRHIVVKCAKKFCNYCKKPG 198 (220)
Q Consensus 172 ~~~~~~~~g~~~~~~~~~~C~~Cgk~G 198 (220)
+|..||..-.. ++..|.+|+.++
T Consensus 31 kC~~CG~v~~P----Pr~~Cp~C~~~~ 53 (140)
T COG1545 31 KCKKCGRVYFP----PRAYCPKCGSET 53 (140)
T ss_pred EcCCCCeEEcC----CcccCCCCCCCC
Confidence 46666654332 345688888876
No 116
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=27.18 E-value=67 Score=17.17 Aligned_cols=26 Identities=19% Similarity=0.448 Sum_probs=14.6
Q ss_pred cccccCCCCCcccccc----cCccccccCC
Q 036141 171 VQCFSCKEYRHIVVKC----AKKFCNYCKK 196 (220)
Q Consensus 171 ~~~~~~~~~g~~~~~~----~~~~C~~Cgk 196 (220)
..|..|+.....+=.- ..-.|+.|+.
T Consensus 4 ~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 4577777766553111 1126888864
No 117
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=27.12 E-value=28 Score=23.78 Aligned_cols=31 Identities=26% Similarity=0.569 Sum_probs=20.3
Q ss_pred CcccccCCCCCcccccccCccccccCCCCcccC
Q 036141 170 QVQCFSCKEYRHIVVKCAKKFCNYCKKPGHIIK 202 (220)
Q Consensus 170 ~~~~~~~~~~g~~~~~~~~~~C~~Cgk~GH~~~ 202 (220)
...|.+|+...+.-.+- -.|-||+.|=+.-+
T Consensus 69 ~V~CP~C~K~TKmLGr~--D~CM~C~~pLTLd~ 99 (114)
T PF11023_consen 69 QVECPNCGKQTKMLGRV--DACMHCKEPLTLDP 99 (114)
T ss_pred eeECCCCCChHhhhchh--hccCcCCCcCccCc
Confidence 34588888876553322 26999998866543
No 118
>PF03902 Gal4_dimer: Gal4-like dimerisation domain; InterPro: IPR005600 The DNA binding domain (residues 1 to 147) of the yeast transcriptional activator GAL4 exists in solution in dimeric form, with the region responsible for dimerisation somewhere between residues 74 and 147. Experimental studies confirmed that the 'hydrophobic region' of the protein (residues 54-97, which contains a larger proportion of alpha-helix), is essential for dimerisation []. ; PDB: 1HBW_B 1D66_A 3COQ_A.
Probab=27.12 E-value=1.4e+02 Score=17.66 Aligned_cols=26 Identities=12% Similarity=0.175 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHhhcccccCCcccH
Q 036141 60 NYFSGFQNLWAEYVDMIYVQVPIESL 85 (220)
Q Consensus 60 ~y~~~~~~l~~~L~~~~~~~~~~~~~ 85 (220)
.|+.++..-...|+.+...-+|+..+
T Consensus 3 aHLTeVE~Rl~~lE~ll~~lfP~~di 28 (57)
T PF03902_consen 3 AHLTEVENRLEKLEQLLRELFPGEDI 28 (57)
T ss_dssp HHHHHHHHHHHHHHHHHCCCSSSSHH
T ss_pred hHHHHHHHHHHHHHHHHHHHCCCcCH
Confidence 46666666666666665555665443
No 119
>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]
Probab=26.62 E-value=29 Score=27.27 Aligned_cols=18 Identities=33% Similarity=0.848 Sum_probs=16.0
Q ss_pred cccccCCCCcccCCCCCCC
Q 036141 190 FCNYCKKPGHIIKECPTRP 208 (220)
Q Consensus 190 ~C~~Cgk~GH~~~~C~~k~ 208 (220)
.|..| +-.||..+||-|.
T Consensus 121 ~CR~C-~gdHwt~~CPyK~ 138 (270)
T KOG0122|consen 121 ACRIC-KGDHWTTNCPYKD 138 (270)
T ss_pred eeeec-CCCeeeecCCchh
Confidence 79999 8999999999654
No 120
>COG4830 RPS26B Ribosomal protein S26 [Translation, ribosomal structure and biogenesis]
Probab=26.55 E-value=42 Score=22.26 Aligned_cols=10 Identities=30% Similarity=0.640 Sum_probs=7.0
Q ss_pred CccccccCCC
Q 036141 188 KKFCNYCKKP 197 (220)
Q Consensus 188 ~~~C~~Cgk~ 197 (220)
...|.+||+.
T Consensus 20 ~v~CdnCg~~ 29 (108)
T COG4830 20 YVRCDNCGKA 29 (108)
T ss_pred ceeecccccc
Confidence 3468888875
No 121
>PF11248 DUF3046: Protein of unknown function (DUF3046); InterPro: IPR021408 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=26.45 E-value=61 Score=19.70 Aligned_cols=20 Identities=20% Similarity=0.504 Sum_probs=15.5
Q ss_pred ccccccHHHHHHHHHHHhcc
Q 036141 16 LKLHKTAKDMWEYLKKVYNQ 35 (220)
Q Consensus 16 ~~~~~ta~~~w~~L~~~f~~ 35 (220)
+..=..++++|..|+..|+.
T Consensus 40 L~~G~dpr~VW~AlC~~~dV 59 (63)
T PF11248_consen 40 LEAGVDPRDVWRALCDAFDV 59 (63)
T ss_pred HHcCCCHHHHHHHHHHHcCC
Confidence 33345789999999999973
No 122
>TIGR00984 3a0801s03tim44 mitochondrial import inner membrane, translocase subunit. translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family is specific for the Tim proteins.
Probab=26.42 E-value=4.1e+02 Score=22.63 Aligned_cols=91 Identities=12% Similarity=0.076 Sum_probs=48.9
Q ss_pred ccHHHHHHHHHHHhccCChhHHhHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHhhcccccCCc----ccHHHHHHHHHH
Q 036141 20 KTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQG-NLSIQNYFSGFQNLWAEYVDMIYVQVPI----ESLADVQEVHEQ 94 (220)
Q Consensus 20 ~ta~~~w~~L~~~f~~~~~~~~~~l~~~~~~~~q~-~~sv~~y~~~~~~l~~~L~~~~~~~~~~----~~~~~~~~~~~~ 94 (220)
..+.+-|..+++.= .+.+.|..++.. ++|=.-.+..++.|-+.+.++++.-+.+ .++..++.++..
T Consensus 170 s~~~~~w~~fk~~~---------~~~~~~~~lk~~~~eSeNp~i~~~r~itdkv~~~~~~lF~ete~a~~l~eIk~~DPs 240 (378)
T TIGR00984 170 SSWYSKVEDFKESN---------VVYRKIQELKKKYDESENPLVRMMRGVTDKIGGVFSGMFSETEVSEVLTEFKKIDPT 240 (378)
T ss_pred cHHHHHHHHHHhhC---------HHHHHHHHHHHHhhcccChhhhHhHHhhhhhhhhhhcccCCCHHHHHHHHHHHhCCC
Confidence 34577787777521 112222222221 3333355666777766665433333322 233334334444
Q ss_pred HHHHHHHhhccch-HHHHHHhhcCCC
Q 036141 95 SKRDQFLMKLRPK-YEAARSNLMNRD 119 (220)
Q Consensus 95 ~~~~~~l~gLp~~-~~~~~~~l~~~~ 119 (220)
--...||.|+... |..|..++...+
T Consensus 241 Fd~~~Fl~gar~aI~p~ILeAf~kGD 266 (378)
T TIGR00984 241 FDKEHFLRFLREYIVPEILEAYVKGD 266 (378)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 4567799999888 777888877653
No 123
>PF12417 DUF3669: Zinc finger protein ; InterPro: IPR022137 This domain family is found in eukaryotes, and is typically between 64 and 80 amino acids in length.
Probab=25.93 E-value=60 Score=20.17 Aligned_cols=20 Identities=25% Similarity=0.604 Sum_probs=16.2
Q ss_pred cccccHHHHHHHHHHHhccC
Q 036141 17 KLHKTAKDMWEYLKKVYNQD 36 (220)
Q Consensus 17 ~~~~ta~~~w~~L~~~f~~~ 36 (220)
...++..++|+.|+..|...
T Consensus 38 ~~~~~~~~lW~~F~~~Yl~~ 57 (72)
T PF12417_consen 38 DCEKTDKELWNQFRSRYLET 57 (72)
T ss_pred ccchHHHHHHHHHHHHHHHH
Confidence 44568899999999999743
No 124
>PF06424 PRP1_N: PRP1 splicing factor, N-terminal; InterPro: IPR010491 This domain is specific to the N-terminal part of the prp1 splicing factor, which is involved in mRNA splicing (and possibly also poly(A)+ RNA nuclear export and cell cycle progression). This domain is specific to the N terminus of the RNA splicing factor encoded by prp1 []. It is involved in mRNA splicing and possibly also poly(A)and RNA nuclear export and cell cycle progression.; GO: 0000398 nuclear mRNA splicing, via spliceosome, 0005634 nucleus
Probab=25.77 E-value=2.5e+02 Score=19.94 Aligned_cols=47 Identities=19% Similarity=0.394 Sum_probs=30.9
Q ss_pred cHHHHHHHHHHHhccC-ChhHHhHHHHHHHHHhcCCccHHHHHHHHHH
Q 036141 21 TAKDMWEYLKKVYNQD-NTAKRSHLEYEIARYSQGNLSIQNYFSGFQN 67 (220)
Q Consensus 21 ta~~~w~~L~~~f~~~-~~~~~~~l~~~~~~~~q~~~sv~~y~~~~~~ 67 (220)
-|..||+.+..+-... ...+...++..........-.|.+.+..|++
T Consensus 64 EAD~Iy~~ID~rmd~Rrk~~re~~~~~e~e~~~~~~pkI~~QFaDLKR 111 (133)
T PF06424_consen 64 EADRIYESIDRRMDSRRKKRREAREKEEIEKYRKENPKIQQQFADLKR 111 (133)
T ss_pred HHHHHHHHHHHHHHhcccchhhhhhhhHHHhhhccCchHHHHHHHHHH
Confidence 5789999999988743 3334455555566666666667766665553
No 125
>PF13512 TPR_18: Tetratricopeptide repeat
Probab=25.38 E-value=2e+02 Score=20.68 Aligned_cols=51 Identities=24% Similarity=0.253 Sum_probs=35.3
Q ss_pred ccccHHHHHHHHHHHhccCChhHHhHHHHHHHHHhcC-CccHHHHHHHHHHH
Q 036141 18 LHKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQG-NLSIQNYFSGFQNL 68 (220)
Q Consensus 18 ~~~ta~~~w~~L~~~f~~~~~~~~~~l~~~~~~~~q~-~~sv~~y~~~~~~l 68 (220)
.+..|.+.|..|..+|-.+.-+...+|..-.....++ -+.-..-+.+|.+|
T Consensus 25 ~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirL 76 (142)
T PF13512_consen 25 NYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRL 76 (142)
T ss_pred CHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence 4678899999999999876666677777777777665 23334444555544
No 126
>PF09133 SANTA: SANTA (SANT Associated); InterPro: IPR015216 The SANTA domain (SANT associated) is approximately 90 amino acids in length and is conserved in eukaryotes. It is sometimes found in association with the SANT domain (IPR001005 from INTERPRO, also known as the Myb-like DNA-binding domain) implying a putative function in regulating chromatin remodelling. Sequence analysis has showed that the SANTA domain is likely to form four central beta-sheets with three flanking alpha-helices. Many conserved hydrophobic residues are present which implies a possible role in protein-protein interactions.
Probab=25.27 E-value=74 Score=20.92 Aligned_cols=21 Identities=10% Similarity=0.178 Sum_probs=16.7
Q ss_pred HHHHHHHHhhccchHHHHHHh
Q 036141 94 QSKRDQFLMKLRPKYEAARSN 114 (220)
Q Consensus 94 ~~~~~~~l~gLp~~~~~~~~~ 114 (220)
...+.+|..|.|+.|+.+...
T Consensus 71 ~~v~~~F~~GFP~~W~~~~~~ 91 (93)
T PF09133_consen 71 SEVIKKFMNGFPENWEEYINE 91 (93)
T ss_pred HHHHHHHhcCCCHHHHHHHHh
Confidence 445667999999999998653
No 127
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=25.02 E-value=44 Score=22.86 Aligned_cols=26 Identities=19% Similarity=0.519 Sum_probs=13.4
Q ss_pred cccccCCCCCcccccccCccccccCCCC
Q 036141 171 VQCFSCKEYRHIVVKCAKKFCNYCKKPG 198 (220)
Q Consensus 171 ~~~~~~~~~g~~~~~~~~~~C~~Cgk~G 198 (220)
..|..|+..... ......|..||.++
T Consensus 71 ~~C~~Cg~~~~~--~~~~~~CP~Cgs~~ 96 (113)
T PRK12380 71 AWCWDCSQVVEI--HQHDAQCPHCHGER 96 (113)
T ss_pred EEcccCCCEEec--CCcCccCcCCCCCC
Confidence 347777643333 22233477777654
No 128
>PF00649 Copper-fist: Copper fist DNA binding domain; InterPro: IPR001083 Some fungal transcription factors contain an N-terminal domain, the copper fist, which seems to be involved in copper-dependent DNA-binding [, ]. These proteins activate the transcription of the metallothionein gene in response to copper. Metallothionein maintains copper levels in yeast [, ]. The copper fist domain, which is similar in structure to metallothionein itself, undergoes a large conformational change on copper-binding that allows DNA-binding. The domain contains a conserved array of zinc-binding residues (Cys-X2-Cys-X8-Cys-X-His) and forms a three-stranded antiparallel beta-sheet with two short helical segments that project from one end of the beta-sheet []. Conserved residues form a basic patch that may be important for DNA binding. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0005507 copper ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1CO4_A.
Probab=24.69 E-value=36 Score=18.55 Aligned_cols=15 Identities=33% Similarity=0.837 Sum_probs=10.2
Q ss_pred ccccCCCCcccCCCCC
Q 036141 191 CNYCKKPGHIIKECPT 206 (220)
Q Consensus 191 C~~Cgk~GH~~~~C~~ 206 (220)
|-.| ..||.+..|.-
T Consensus 11 C~~C-irGHRss~C~H 25 (40)
T PF00649_consen 11 CESC-IRGHRSSTCNH 25 (40)
T ss_dssp ETTT-TTTSGGGG---
T ss_pred hhhh-hCccccCcccC
Confidence 7777 78999999953
No 129
>PF07851 TMPIT: TMPIT-like protein; InterPro: IPR012926 A number of members of this family are annotated as being transmembrane proteins induced by tumour necrosis factor alpha, but no literature was found to support this. ; GO: 0016021 integral to membrane
Probab=24.55 E-value=3.3e+02 Score=22.66 Aligned_cols=66 Identities=15% Similarity=0.246 Sum_probs=38.6
Q ss_pred HHHHHHHHHhcc-CChhHHhHHHHH-HHHHhcC-CccHHHHHHHHHHHHHHHhhcccccCCcccHHHHHH
Q 036141 24 DMWEYLKKVYNQ-DNTAKRSHLEYE-IARYSQG-NLSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQE 90 (220)
Q Consensus 24 ~~w~~L~~~f~~-~~~~~~~~l~~~-~~~~~q~-~~sv~~y~~~~~~l~~~L~~~~~~~~~~~~~~~~~~ 90 (220)
+=|+.|.+.|.. ....+.+..+.+ +...... ..+|.....+++.|...|+.. ....+.+....+.+
T Consensus 4 eEW~eL~~efq~Lqethr~Y~qKleel~~lQ~~C~ssI~~QkkrLk~L~~sLk~~-~~~~~~e~~~~i~~ 72 (330)
T PF07851_consen 4 EEWEELQKEFQELQETHRSYKQKLEELSKLQDKCSSSISHQKKRLKELKKSLKRC-KKSLSAEERELIEK 72 (330)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-ccCCChhHHHHHHH
Confidence 448888888874 222333333332 3333333 678888888999999988865 33334444444443
No 130
>PRK05667 dnaG DNA primase; Validated
Probab=24.47 E-value=46 Score=29.95 Aligned_cols=30 Identities=20% Similarity=0.223 Sum_probs=16.8
Q ss_pred ccccCCCCCcccc---cccCccccccCCCCccc
Q 036141 172 QCFSCKEYRHIVV---KCAKKFCNYCKKPGHII 201 (220)
Q Consensus 172 ~~~~~~~~g~~~~---~~~~~~C~~Cgk~GH~~ 201 (220)
.|..|+....+-. ....-+||.||..|-..
T Consensus 38 ~CPfH~ektpSf~V~~~k~~~~CF~Cg~~Gd~i 70 (580)
T PRK05667 38 LCPFHDEKTPSFTVSPDKQFYHCFGCGAGGDVI 70 (580)
T ss_pred cCCCCCCCCCceEEECCCCeEEECCCCCCCCHH
Confidence 4666665543322 12223799999988543
No 131
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=24.43 E-value=29 Score=18.95 Aligned_cols=11 Identities=55% Similarity=1.241 Sum_probs=4.8
Q ss_pred ccccCCCCccc
Q 036141 191 CNYCKKPGHII 201 (220)
Q Consensus 191 C~~Cgk~GH~~ 201 (220)
|.+||+++...
T Consensus 1 C~~C~~~~~~~ 11 (47)
T PF01844_consen 1 CQYCGKPGSDN 11 (47)
T ss_dssp -TTT--B--GG
T ss_pred CCCCCCcCccC
Confidence 78899988765
No 132
>PF06874 FBPase_2: Firmicute fructose-1,6-bisphosphatase; InterPro: IPR009164 Fructose 1,6-bisphosphatase catalyses the hydrolysis of fructose 1,6-bisphosphate to fructose 6-phosphate []. This is an essential reaction in the process of gluconeogenesis, the process by which non-carbohydrate precursors are converted to glucose, and hence this enzyme is found almost universally. Enzyme activity can be regulated by a number of different mechanisms including AMP inhibition, cylic AMP-dependent phosphorylation and light-dependent-activation. This entry represents a group of fructose 1,6-bisphosphatases found within the Firmicutes (low GC Gram-positive bacteria) which do not show any significant sequence similarity to the enzymes from other organisms. The Bacillus subtilis enzyme is inhibited by AMP, though this can be overcome by phosphoenolpyruvate, and is dependent on Mn(2+) [, ]. Mutants lacking this enzyme are apparently still able to grow on gluconeogenic growth substrates such as malate and glycerol.; GO: 0042132 fructose 1,6-bisphosphate 1-phosphatase activity, 0006094 gluconeogenesis
Probab=24.32 E-value=5.6e+02 Score=23.49 Aligned_cols=81 Identities=9% Similarity=0.139 Sum_probs=49.1
Q ss_pred HHHHHHHHhccC-Chh-------HHhHHHHHHHHHhcCCccHHHHH-HHHHHHHHHHhhcccccCCcccHHHHHHHHHHH
Q 036141 25 MWEYLKKVYNQD-NTA-------KRSHLEYEIARYSQGNLSIQNYF-SGFQNLWAEYVDMIYVQVPIESLADVQEVHEQS 95 (220)
Q Consensus 25 ~w~~L~~~f~~~-~~~-------~~~~l~~~~~~~~q~~~sv~~y~-~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~ 95 (220)
+-..+.+.|... +.. .++.-+.++...++..+...+|+ .-+..|+.=++ +... ..
T Consensus 59 Ir~KI~~~F~~~l~~~e~~~LatLIYYP~ekl~~~~~~~~~~~~Wy~~tl~rLi~l~k-~vss---------------KY 122 (640)
T PF06874_consen 59 IREKIDELFGDTLSEEEKRELATLIYYPEEKLELLKKEEEDLDEWYRITLYRLIELCK-FVSS---------------KY 122 (640)
T ss_pred HHHHHHHHhcccCCHHHHHHHHHHhcCHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHH-HHhc---------------cc
Confidence 445666777632 211 23344555666666667788876 34445544443 2122 23
Q ss_pred HHHHHHhhccchHHHHHHhhcCCCCC
Q 036141 96 KRDQFLMKLRPKYEAARSNLMNRDLS 121 (220)
Q Consensus 96 ~~~~~l~gLp~~~~~~~~~l~~~~~~ 121 (220)
-+.++...||++|.-+.+.|+...+.
T Consensus 123 TRSKVRKalP~~faYIieELL~~~~~ 148 (640)
T PF06874_consen 123 TRSKVRKALPKDFAYIIEELLHEDDE 148 (640)
T ss_pred cHHHHHHhCCHhHHHHHHHHhcCCCC
Confidence 34568889999999999999986654
No 133
>PRK14291 chaperone protein DnaJ; Provisional
Probab=24.20 E-value=79 Score=26.73 Aligned_cols=39 Identities=18% Similarity=0.383 Sum_probs=23.2
Q ss_pred cccccCCCCCccccc----ccCccccccCCCCcccCCCCCCCC
Q 036141 171 VQCFSCKEYRHIVVK----CAKKFCNYCKKPGHIIKECPTRPQ 209 (220)
Q Consensus 171 ~~~~~~~~~g~~~~~----~~~~~C~~Cgk~GH~~~~C~~k~~ 209 (220)
..|..|.+.|..... .....|..|+-.|-+...|+.-..
T Consensus 174 ~~C~~C~G~G~~~~~~g~~~~~~~C~~C~G~G~~~~~C~~C~G 216 (382)
T PRK14291 174 KVCPTCGGSGEIYQRGGFFRISQTCPTCGGEGVLREPCSKCNG 216 (382)
T ss_pred ccCCCCCCceEEEEecceEEEEecCCCCCCceEEccCCCCCCC
Confidence 346666665543221 112368999999977777876543
No 134
>PF07023 DUF1315: Protein of unknown function (DUF1315); InterPro: IPR009749 This family consists of several bacterial proteins of around 90 residues in length. The function of this family is unknown.
Probab=24.10 E-value=57 Score=21.52 Aligned_cols=19 Identities=21% Similarity=0.440 Sum_probs=16.8
Q ss_pred HHHhhccch-HHHHHHhhcC
Q 036141 99 QFLMKLRPK-YEAARSNLMN 117 (220)
Q Consensus 99 ~~l~gLp~~-~~~~~~~l~~ 117 (220)
.+|..|+|+ |+.++.++..
T Consensus 3 ~li~~mtPevY~rL~~AVEl 22 (93)
T PF07023_consen 3 QLIDSMTPEVYERLKQAVEL 22 (93)
T ss_pred HHHHhCCHHHHHHHHHHHHh
Confidence 488999988 9999999977
No 135
>PF02093 Gag_p30: Gag P30 core shell protein; InterPro: IPR003036 P30 is essential for viral assembly []. Cleavage of P70 in vitro can be accompanied by a shift from a concentrically coiled internal strand ("immature") to a collapsed ("mature") form of the virus core [].; GO: 0019068 virion assembly; PDB: 3BP9_U 1U7K_D 2Y4Z_A 1BM4_A.
Probab=23.75 E-value=60 Score=24.92 Aligned_cols=28 Identities=18% Similarity=0.430 Sum_probs=20.2
Q ss_pred HHHHhcC-CccHHHHHHHHHHHHHHHhhc
Q 036141 48 IARYSQG-NLSIQNYFSGFQNLWAEYVDM 75 (220)
Q Consensus 48 ~~~~~q~-~~sv~~y~~~~~~l~~~L~~~ 75 (220)
+....|+ +||...|+.+++..+.....+
T Consensus 129 v~~v~Qg~~EsPs~FLeRL~ea~r~yTp~ 157 (211)
T PF02093_consen 129 VREVTQGPNESPSAFLERLREAYRKYTPF 157 (211)
T ss_dssp --TTTTTGGGHHHHHHHHHHHHHHHTS--
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHHhcCCC
Confidence 4445676 999999999999888777644
No 136
>KOG0403 consensus Neoplastic transformation suppressor Pdcd4/MA-3, contains MA3 domain [Signal transduction mechanisms]
Probab=23.45 E-value=2.2e+02 Score=24.94 Aligned_cols=15 Identities=20% Similarity=0.069 Sum_probs=10.6
Q ss_pred HHHHHHHhhccchHH
Q 036141 95 SKRDQFLMKLRPKYE 109 (220)
Q Consensus 95 ~~~~~~l~gLp~~~~ 109 (220)
..++++|..|||+|-
T Consensus 616 G~i~~~l~~~~~s~l 630 (645)
T KOG0403|consen 616 GIISKQLRDLCPSRL 630 (645)
T ss_pred CchhHHhhhcchhhh
Confidence 346668888888754
No 137
>cd01093 CRIB_PAK_like PAK (p21 activated kinase) Binding Domain (PBD), binds Cdc42p- and/or Rho-like small GTPases; also known as the Cdc42/Rac interactive binding (CRIB) motif; has been shown to inhibit transcriptional activation and cell transformation mediated by the Ras-Rac pathway. This subgroup of CRIB/PBD-domains is found N-terminal of Serine/Threonine kinase domains in PAK and PAK-like proteins.
Probab=23.39 E-value=50 Score=18.50 Aligned_cols=14 Identities=7% Similarity=0.166 Sum_probs=11.5
Q ss_pred HhhccchHHHHHHh
Q 036141 101 LMKLRPKYEAARSN 114 (220)
Q Consensus 101 l~gLp~~~~~~~~~ 114 (220)
+.|||++|..+..+
T Consensus 24 f~glP~eW~~ll~~ 37 (46)
T cd01093 24 FTGLPEEWQRLLKS 37 (46)
T ss_pred ccCCCHHHHHHHHH
Confidence 38999999988665
No 138
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=23.31 E-value=45 Score=18.56 Aligned_cols=26 Identities=27% Similarity=0.650 Sum_probs=15.1
Q ss_pred cccccCCCCCcccccc-cCccccccCC
Q 036141 171 VQCFSCKEYRHIVVKC-AKKFCNYCKK 196 (220)
Q Consensus 171 ~~~~~~~~~g~~~~~~-~~~~C~~Cgk 196 (220)
..|.+|+...+..-.. ..-.|..|++
T Consensus 19 ~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 3488888774443222 3336877765
No 139
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=23.28 E-value=49 Score=22.67 Aligned_cols=27 Identities=19% Similarity=0.266 Sum_probs=14.8
Q ss_pred cccccCCCCCcccccccCccccccCCCCc
Q 036141 171 VQCFSCKEYRHIVVKCAKKFCNYCKKPGH 199 (220)
Q Consensus 171 ~~~~~~~~~g~~~~~~~~~~C~~Cgk~GH 199 (220)
..|..|+..... ......|..||.++.
T Consensus 71 ~~C~~Cg~~~~~--~~~~~~CP~Cgs~~~ 97 (115)
T TIGR00100 71 CECEDCSEEVSP--EIDLYRCPKCHGIML 97 (115)
T ss_pred EEcccCCCEEec--CCcCccCcCCcCCCc
Confidence 447777744333 122345777876653
No 140
>PF05667 DUF812: Protein of unknown function (DUF812); InterPro: IPR008530 This family consists of several eukaryotic proteins of unknown function.
Probab=23.22 E-value=1.6e+02 Score=26.68 Aligned_cols=99 Identities=11% Similarity=0.108 Sum_probs=48.4
Q ss_pred cccHHHHHHHHHHHhc--cCChhHHhHHHHH---HHHHhcCCccHHHHHHHHHHHHHHHhhccccc-----C-CcccHHH
Q 036141 19 HKTAKDMWEYLKKVYN--QDNTAKRSHLEYE---IARYSQGNLSIQNYFSGFQNLWAEYVDMIYVQ-----V-PIESLAD 87 (220)
Q Consensus 19 ~~ta~~~w~~L~~~f~--~~~~~~~~~l~~~---~~~~~q~~~sv~~y~~~~~~l~~~L~~~~~~~-----~-~~~~~~~ 87 (220)
...-.+....|...|. ++...|-.+.++- ..+.++..+.|..=+...+.|-.+++.+.|.- + .+-+...
T Consensus 463 ~~~Kee~~~qL~~e~e~~~k~~~Rs~Yt~RIlEIv~NI~KQk~eI~KIl~DTr~lQkeiN~l~gkL~RtF~v~dElifrd 542 (594)
T PF05667_consen 463 IRQKEELYKQLVKELEKLPKDVNRSAYTRRILEIVKNIRKQKEEIEKILSDTRELQKEINSLTGKLDRTFTVTDELIFRD 542 (594)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence 3344556666666666 2333333333332 33444445566666666666666665442210 0 1111111
Q ss_pred HHHHHHHHHHHHHHhhccchHHHHHHhhcC
Q 036141 88 VQEVHEQSKRDQFLMKLRPKYEAARSNLMN 117 (220)
Q Consensus 88 ~~~~~~~~~~~~~l~gLp~~~~~~~~~l~~ 117 (220)
.++-.-..+.++.|..|.+.|..++..+..
T Consensus 543 AKkDe~~rkaYK~La~lh~~c~~Li~~v~~ 572 (594)
T PF05667_consen 543 AKKDEAARKAYKLLASLHENCSQLIETVEE 572 (594)
T ss_pred hhcCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 221112334566788887777777666543
No 141
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=23.21 E-value=2.4e+02 Score=20.14 Aligned_cols=30 Identities=17% Similarity=0.062 Sum_probs=19.0
Q ss_pred ccccccHHHHHHHHHHHhccCChhHHhHHH
Q 036141 16 LKLHKTAKDMWEYLKKVYNQDNTAKRSHLE 45 (220)
Q Consensus 16 ~~~~~ta~~~w~~L~~~f~~~~~~~~~~l~ 45 (220)
-....||.++.+.|++.+-.-+.+.+|+.-
T Consensus 33 ~~~~~sAeei~~~l~~~~p~islaTVYr~L 62 (145)
T COG0735 33 ADGHLSAEELYEELREEGPGISLATVYRTL 62 (145)
T ss_pred cCCCCCHHHHHHHHHHhCCCCCHhHHHHHH
Confidence 334467777777777776666666655433
No 142
>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]
Probab=23.21 E-value=4.3e+02 Score=24.96 Aligned_cols=104 Identities=17% Similarity=0.134 Sum_probs=67.7
Q ss_pred HHHHHHHHHHHhccCChhHHhHHHHHHHHHhcCCccHHHHHHHHHHHHHHHhhcccccCCcccHHHHHHHHHHHHHHHHH
Q 036141 22 AKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQGNLSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFL 101 (220)
Q Consensus 22 a~~~w~~L~~~f~~~~~~~~~~l~~~~~~~~q~~~sv~~y~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 101 (220)
+.+.|+..++.|++. ..|.++|+...-+.=|+.+=+.-++.|...+..+.++.++++++.....+.++.+-.
T Consensus 304 GATT~~EYRk~iEKD-----~AL~RRFQ~V~V~EPs~e~ti~ILrGlk~~yE~hH~V~i~D~Al~aAv~LS~RYI~d--- 375 (786)
T COG0542 304 GATTLDEYRKYIEKD-----AALERRFQKVLVDEPSVEDTIAILRGLKERYEAHHGVRITDEALVAAVTLSDRYIPD--- 375 (786)
T ss_pred EeccHHHHHHHhhhc-----hHHHhcCceeeCCCCCHHHHHHHHHHHHHHHHHccCceecHHHHHHHHHHHHhhccc---
Confidence 356677777777654 456677777777778999999999999999998888888888877775444444333
Q ss_pred hhccchHHHHHHhh----cCC-CCCCCHHHHHHHHHH
Q 036141 102 MKLRPKYEAARSNL----MNR-DLSPSLDVCFKELLR 133 (220)
Q Consensus 102 ~gLp~~~~~~~~~l----~~~-~~~~sl~e~~~~l~~ 133 (220)
+-||+.--.+.+.. ... ..+..++++-.++.+
T Consensus 376 R~LPDKAIDLiDeA~a~~~l~~~~p~~l~~~~~~~~~ 412 (786)
T COG0542 376 RFLPDKAIDLLDEAGARVRLEIDKPEELDELERELAQ 412 (786)
T ss_pred CCCCchHHHHHHHHHHHHHhcccCCcchhHHHHHHHH
Confidence 34565533333321 111 134456666655554
No 143
>PF10664 NdhM: Cyanobacterial and plastid NDH-1 subunit M; InterPro: IPR018922 The NADH dehydrogenase I complex shuttles electrons from an unknown electron donor, via FMN and iron-sulphur (Fe-S) centres, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in plants is believed to be plastoquinone. The NADH dehydrogenase I complex couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. This entry represents subunit M of the NADH dehydrogenase I complex in cyanobacteria and plant chloroplasts []. ; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0055114 oxidation-reduction process
Probab=23.07 E-value=1.7e+02 Score=19.65 Aligned_cols=44 Identities=16% Similarity=0.212 Sum_probs=24.1
Q ss_pred CccHHHHHHHHHHHHHHHhhcccccCCcccHHHHHHHHHHHHHHHHHhhccchHHHHHHhhcC
Q 036141 55 NLSIQNYFSGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMN 117 (220)
Q Consensus 55 ~~sv~~y~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~gLp~~~~~~~~~l~~ 117 (220)
++++..-..+|..|+.... |.++++. -|+.+.++.+.++..++.
T Consensus 41 ~~~l~kVy~~F~eLVe~~~---G~~LtdY----------------nLRrIGSdLE~~iR~LLq 84 (108)
T PF10664_consen 41 EEALQKVYRKFDELVESYA---GEDLTDY----------------NLRRIGSDLEHFIRSLLQ 84 (108)
T ss_pred HHHHHHHHHHHHHHHHhhc---CCCchhh----------------hHHHhccHHHHHHHHHHH
Confidence 4455566666666665554 6555553 244445555555555544
No 144
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=22.99 E-value=56 Score=27.67 Aligned_cols=35 Identities=17% Similarity=0.273 Sum_probs=25.7
Q ss_pred CCCCCCcccccCCCCCcccccccCccccccCCCCcccC
Q 036141 165 GRDMRQVQCFSCKEYRHIVVKCAKKFCNYCKKPGHIIK 202 (220)
Q Consensus 165 ~~~~~~~~~~~~~~~g~~~~~~~~~~C~~Cgk~GH~~~ 202 (220)
+...+...|..|...+... .++.|..||.++|..+
T Consensus 215 ~~~~~~~~C~~C~~~~~~~---~~~~CpRC~~~Ly~rr 249 (418)
T COG2995 215 GAREGLRSCLCCHYILPHD---AEPRCPRCGSKLYVRR 249 (418)
T ss_pred CCcccceecccccccCCHh---hCCCCCCCCChhhccC
Confidence 3444556688888877653 5567999999999866
No 145
>PRK02935 hypothetical protein; Provisional
Probab=22.71 E-value=46 Score=22.46 Aligned_cols=30 Identities=23% Similarity=0.537 Sum_probs=19.4
Q ss_pred cccccCCCCCcccccccCccccccCCCCcccC
Q 036141 171 VQCFSCKEYRHIVVKCAKKFCNYCKKPGHIIK 202 (220)
Q Consensus 171 ~~~~~~~~~g~~~~~~~~~~C~~Cgk~GH~~~ 202 (220)
..|.+|.+..+.-.+ .-.|-||++|=+.-+
T Consensus 71 V~CP~C~K~TKmLGr--vD~CM~C~~PLTLd~ 100 (110)
T PRK02935 71 VICPSCEKPTKMLGR--VDACMHCNQPLTLDR 100 (110)
T ss_pred eECCCCCchhhhccc--eeecCcCCCcCCcCc
Confidence 458888876654222 226999998866543
No 146
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=22.70 E-value=60 Score=15.28 Aligned_cols=10 Identities=30% Similarity=0.776 Sum_probs=6.9
Q ss_pred CccccccCCC
Q 036141 188 KKFCNYCKKP 197 (220)
Q Consensus 188 ~~~C~~Cgk~ 197 (220)
...|+.|+.+
T Consensus 16 ~~~C~~C~~p 25 (26)
T smart00547 16 RSKCFACGAP 25 (26)
T ss_pred hccccccCCc
Confidence 3468888765
No 147
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=22.55 E-value=69 Score=21.20 Aligned_cols=8 Identities=25% Similarity=0.879 Sum_probs=5.5
Q ss_pred ccccccCC
Q 036141 189 KFCNYCKK 196 (220)
Q Consensus 189 ~~C~~Cgk 196 (220)
..|.+||.
T Consensus 21 V~C~nCgr 28 (95)
T PRK09335 21 VQCDNCGR 28 (95)
T ss_pred EEeCCCCC
Confidence 35888875
No 148
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=22.18 E-value=2.4e+02 Score=18.76 Aligned_cols=29 Identities=24% Similarity=0.135 Sum_probs=20.3
Q ss_pred cccccHHHHHHHHHHHhccCChhHHhHHH
Q 036141 17 KLHKTAKDMWEYLKKVYNQDNTAKRSHLE 45 (220)
Q Consensus 17 ~~~~ta~~~w~~L~~~f~~~~~~~~~~l~ 45 (220)
...-||.++|+.|++....-+.+.+++.-
T Consensus 14 ~~~~sa~ei~~~l~~~~~~i~~~TVYR~L 42 (116)
T cd07153 14 DGHLTAEEIYERLRKKGPSISLATVYRTL 42 (116)
T ss_pred CCCCCHHHHHHHHHhcCCCCCHHHHHHHH
Confidence 45678999999999876555555555433
No 149
>PRK08334 translation initiation factor IF-2B subunit beta; Validated
Probab=22.10 E-value=4.8e+02 Score=21.98 Aligned_cols=64 Identities=9% Similarity=0.031 Sum_probs=41.7
Q ss_pred ccccccHHHHHHHHHHHhccCChhH-HhHHHHHHHHHhc-CCccHHHHHHHHHHHHHHHhhccccc
Q 036141 16 LKLHKTAKDMWEYLKKVYNQDNTAK-RSHLEYEIARYSQ-GNLSIQNYFSGFQNLWAEYVDMIYVQ 79 (220)
Q Consensus 16 ~~~~~ta~~~w~~L~~~f~~~~~~~-~~~l~~~~~~~~q-~~~sv~~y~~~~~~l~~~L~~~~~~~ 79 (220)
+..+.+..++|..++++--....+- +....--.....+ .+.++.+|...|......|.+..+..
T Consensus 38 ~~~~~~~~~v~~aI~~M~vRGApaIgvaAa~glal~~~~~~~~~~~~~~~~l~~~~~~L~~~RPTa 103 (356)
T PRK08334 38 VIELRTVEEVAEAIKTMTVRGAPAIGAAAAFGLALYAETSKAKTKDEFMDGFYKAYETLKNTRPTA 103 (356)
T ss_pred EEEeCCHHHHHHHHHhCcccCcHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHHHHHcCCcH
Confidence 4457899999999999887665543 1111111111122 24588999999999999998665443
No 150
>TIGR01623 put_zinc_LRP1 putative zinc finger domain, LRP1 type. This model represents a putative zinc finger domain found in plants. Arabidopsis thaliana has at least 10 distinct members. Proteins containing this domain, including LRP1, generally share the same size, about 300 amino acids, and architecture. This 43-residue domain, and a more C-terminal companion domain of similar size, appear as tightly conserved islands of sequence similarity. The remainder consists largely of low-complexity sequence. Several animal proteins have regions with matching patterns of Cys, Gly, and His residues. These are not included in the model but score between trusted and noise cutoffs.
Probab=21.83 E-value=43 Score=18.53 Aligned_cols=23 Identities=26% Similarity=0.657 Sum_probs=11.9
Q ss_pred cccCCCCCcccccccCccccccCCC
Q 036141 173 CFSCKEYRHIVVKCAKKFCNYCKKP 197 (220)
Q Consensus 173 ~~~~~~~g~~~~~~~~~~C~~Cgk~ 197 (220)
|..|+++... .|....|..|-|.
T Consensus 2 C~~CgNpa~k--~C~~~~CRtCCK~ 24 (43)
T TIGR01623 2 CQDCGNQAKK--ECLFERCRTCCKS 24 (43)
T ss_pred hhhccchhhC--CCchhhhhHHhcc
Confidence 3445554443 5666666665443
No 151
>PF09180 ProRS-C_1: Prolyl-tRNA synthetase, C-terminal; InterPro: IPR016061 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Prolyl tRNA synthetase (6.1.1.15 from EC) exists in two forms, which are loosely related. The first form is present in the majority of eubacteria species. The second one, present in some eubacteria, is essentially present in archaea and eukaryota. Prolyl-tRNA synthetase belongs to class IIa. This domain is found at the C-terminal in archaeal and eukaryotic enzymes, as well as in certain bacterial ones.; GO: 0000166 nucleotide binding, 0004827 proline-tRNA ligase activity, 0005524 ATP binding, 0006433 prolyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1NJ6_A 1NJ2_A 1NJ5_A 1NJ1_A 1H4T_C 1H4S_A 1HC7_C 1H4Q_B 3IAL_B.
Probab=21.81 E-value=38 Score=20.76 Aligned_cols=13 Identities=31% Similarity=0.626 Sum_probs=6.6
Q ss_pred cCccccccCCCCc
Q 036141 187 AKKFCNYCKKPGH 199 (220)
Q Consensus 187 ~~~~C~~Cgk~GH 199 (220)
...+|.+||++.-
T Consensus 47 ~~~~Ci~cgk~a~ 59 (68)
T PF09180_consen 47 EGGKCIVCGKPAK 59 (68)
T ss_dssp TT-B-TTT-SB-S
T ss_pred CCCeeecCCChhh
Confidence 3457999998864
No 152
>cd07562 Peptidase_S41_TRI Tricorn protease; serine protease family S41. The tricorn protease (TRI), a member of the S41 peptidase family and named for its tricorn-like shape, exists only in some archaea and eubacteria. It has been shown to act as a carboxypeptidase, involved in the degradation of proteasomal products to preferentially yield di- and tripeptides, with subsequent and final degradations to free amino acid residues by tricorn interacting factors, F1, F2 and F3. Tricorn is a hexameric D3-symmetric protease of 720kD, and can self-associate further into a giant icosahedral capsid structure containing twenty copies of the complex. Each tricorn peptidase monomer consists of five structural domains: a six-bladed beta-propeller and a seven-bladed beta-propeller that limit access to the active site, the two domains (C1 and C2) that carry the active site residues, and a PDZ-like domain (proposed to be important for substrate recognition) between the C1 and C2 domains. The active sit
Probab=21.79 E-value=3e+02 Score=21.71 Aligned_cols=54 Identities=7% Similarity=0.152 Sum_probs=38.0
Q ss_pred cHHHHHHHHHHHhccCC--hhHHhHHHHHHHHHhcCCccHHHHHHHHHHHHHHHhh
Q 036141 21 TAKDMWEYLKKVYNQDN--TAKRSHLEYEIARYSQGNLSIQNYFSGFQNLWAEYVD 74 (220)
Q Consensus 21 ta~~~w~~L~~~f~~~~--~~~~~~l~~~~~~~~q~~~sv~~y~~~~~~l~~~L~~ 74 (220)
...++|..+++.|-... ..--..++.++.-....-.+-.++..-|..+..+|.+
T Consensus 5 ~fd~~w~~~~~~y~~~~~~g~dW~~~~~~y~~~~~~~~~~~e~~~~l~~ml~~L~d 60 (266)
T cd07562 5 MFDEAWRLVRDNFYDPDMHGVDWDAVRAEYRPLLPRAATRAELADVLNEMLGELND 60 (266)
T ss_pred HHHHHHHHHHhhccCCCCCCCCHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHcC
Confidence 45789999999986322 1222345555666555667889999999999998874
No 153
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=21.64 E-value=95 Score=17.81 Aligned_cols=29 Identities=17% Similarity=0.368 Sum_probs=15.8
Q ss_pred ccccCCCCCcccc---c---ccC-ccccccCCCCcc
Q 036141 172 QCFSCKEYRHIVV---K---CAK-KFCNYCKKPGHI 200 (220)
Q Consensus 172 ~~~~~~~~g~~~~---~---~~~-~~C~~Cgk~GH~ 200 (220)
.|..||+...... . ... ..|..||-.|..
T Consensus 3 PCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 3 PCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCcceeeEeccCCCCCEEEEECCCCCCCccc
Confidence 4778887766221 1 111 147777766654
No 154
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=21.61 E-value=72 Score=21.64 Aligned_cols=8 Identities=25% Similarity=0.800 Sum_probs=5.6
Q ss_pred ccccccCC
Q 036141 189 KFCNYCKK 196 (220)
Q Consensus 189 ~~C~~Cgk 196 (220)
..|.+||+
T Consensus 21 V~C~nCgr 28 (108)
T PTZ00172 21 VRCSNCGR 28 (108)
T ss_pred EEeCCccc
Confidence 35888875
No 155
>PLN00186 ribosomal protein S26; Provisional
Probab=21.52 E-value=74 Score=21.59 Aligned_cols=8 Identities=38% Similarity=0.804 Sum_probs=5.5
Q ss_pred ccccccCC
Q 036141 189 KFCNYCKK 196 (220)
Q Consensus 189 ~~C~~Cgk 196 (220)
..|.+||+
T Consensus 21 V~C~nCgr 28 (109)
T PLN00186 21 IRCSNCGK 28 (109)
T ss_pred eeeCCCcc
Confidence 35888875
No 156
>COG3120 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.30 E-value=1.7e+02 Score=20.51 Aligned_cols=16 Identities=31% Similarity=0.636 Sum_probs=12.1
Q ss_pred ccccccchHHHHhhcc
Q 036141 2 TWIMGSIDQSLILNLK 17 (220)
Q Consensus 2 s~i~~sl~~~~~~~~~ 17 (220)
+||-.+|+|.+...+.
T Consensus 56 ~WI~~Hmsp~L~~klk 71 (149)
T COG3120 56 EWIDAHMSPELVNKLK 71 (149)
T ss_pred HHHHHhcCHHHHHHHH
Confidence 5788888888877654
No 157
>COG1151 6Fe-6S prismane cluster-containing protein [Energy production and conversion]
Probab=21.13 E-value=2.3e+02 Score=25.39 Aligned_cols=72 Identities=14% Similarity=-0.008 Sum_probs=49.5
Q ss_pred HHHHHHHHHHhhcccccCCcccHHHHHHHHHHHHHHHHHhhccchHHHHHHhhcCCCCCCCHHHHHHHHHHHHHH
Q 036141 63 SGFQNLWAEYVDMIYVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNLMNRDLSPSLDVCFKELLREEQR 137 (220)
Q Consensus 63 ~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~gLp~~~~~~~~~l~~~~~~~sl~e~~~~l~~~e~~ 137 (220)
-++..|+..|....|.++|+=-++..-+|.|+..+...+..| +--+........+..+..+.+..++.+.-.
T Consensus 474 ~r~~~la~aLae~lgvdI~dLPia~~a~WmEQKAv~~l~~lL---~lGvknihvgP~pp~~gs~~v~kvL~e~~~ 545 (576)
T COG1151 474 YRIIVLALALAEVLGLDINDLPLALVASWMEQKAVIDLLFLL---SLGVKNIHVGPTPPVFGSPDVTKVLTEDFG 545 (576)
T ss_pred HHHHHHHHHHHHHhCCCCccccHHHHHHHHHHHHHHHHHHHH---HcCCcceeeCCCCcccCCHHHHHHHHhhcC
Confidence 455566677777778888775555555889998888877766 334443455667777788888887777643
No 158
>TIGR03044 PS_II_psb27 photosystem II protein Psb27. Members of this family are the Psb27 protein of the cyanobacterial photosynthetic supracomplex, photosystem II. Although most protein components of both cyanobacterial and chloroplast versions of photosystem II are closely related and described together by single model families, this family is strictly bacterial. Some uncharacterized proteins with highly divergent sequences, from Arabidopsis, score between trusted and noise cutoffs for this model but are not at this time assigned as functionally equivalent photosystem II proteins.
Probab=21.12 E-value=3.2e+02 Score=19.47 Aligned_cols=33 Identities=15% Similarity=0.166 Sum_probs=16.5
Q ss_pred HhhccchHHHHHHhhcC-------CCCCCCHHHHHHHHHHH
Q 036141 101 LMKLRPKYEAARSNLMN-------RDLSPSLDVCFKELLRE 134 (220)
Q Consensus 101 l~gLp~~~~~~~~~l~~-------~~~~~sl~e~~~~l~~~ 134 (220)
+.|||+ |.++.++|.. ....|--+++.++|..|
T Consensus 85 v~g~~S-Fttm~TALNsLAGHY~sy~~rPlPeklk~Rl~~E 124 (135)
T TIGR03044 85 VNGLSS-FTTMQTALNSLAGHYKSYANRPLPEKLKERLEKE 124 (135)
T ss_pred cCCccc-HHHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHH
Confidence 556654 7766665522 11223335666665443
No 159
>PF08203 RNA_polI_A14: Yeast RNA polymerase I subunit RPA14; InterPro: IPR013239 Saccharomyces cerevisiae RNA polymerase I (Pol I) is a complex consisting of 14 subunits. Subunit RPA14 forms part of a Pol I subcomplex consisting of RPA14 and and RPA43. The RPA14 and RPA43 heterodimer is proposed to play a role in the recruitment of Pol I to the promoter []. ; PDB: 2RF4_F.
Probab=21.04 E-value=56 Score=20.67 Aligned_cols=16 Identities=19% Similarity=0.169 Sum_probs=9.4
Q ss_pred HHHHHHHHHHhhccch
Q 036141 92 HEQSKRDQFLMKLRPK 107 (220)
Q Consensus 92 ~~~~~~~~~l~gLp~~ 107 (220)
..-.+|.+-|+||||.
T Consensus 59 SQLKRiQRdlrGLPP~ 74 (76)
T PF08203_consen 59 SQLKRIQRDLRGLPPL 74 (76)
T ss_dssp HHHHHHHHHHHHS---
T ss_pred HHHHHHHHhhCCCCCC
Confidence 3445677789999984
No 160
>PF05879 RHD3: Root hair defective 3 GTP-binding protein (RHD3); InterPro: IPR008803 This family consists of several eukaryotic root hair defective 3 like GTP-binding proteins. It has been speculated that the RHD3 protein is a member of a novel class of GTP-binding proteins that is widespread in eukaryotes and required for regulated cell enlargement []. The family also contains the homologous Saccharomyces cerevisiae synthetic construct enhancement of YOP1 (SEY1) protein which is involved in membrane trafficking [].; GO: 0016817 hydrolase activity, acting on acid anhydrides
Probab=20.89 E-value=2.3e+02 Score=26.50 Aligned_cols=60 Identities=10% Similarity=0.273 Sum_probs=33.6
Q ss_pred cchHHHHhhccccccHHHHHHHHHHHhccCChhHHhHHHHHHHHHhcCCccHHHHHHHHHHH
Q 036141 7 SIDQSLILNLKLHKTAKDMWEYLKKVYNQDNTAKRSHLEYEIARYSQGNLSIQNYFSGFQNL 68 (220)
Q Consensus 7 sl~~~~~~~~~~~~ta~~~w~~L~~~f~~~~~~~~~~l~~~~~~~~q~~~sv~~y~~~~~~l 68 (220)
.|.+.+...+.. ...++|+.+.+.|..........+......+--..+.+.+++.+|+.-
T Consensus 437 ~l~e~v~~~l~~--~~~d~Wd~I~~~f~~~~~~~~~~~~~~~~~f~~s~~e~~~~~~~lr~~ 496 (742)
T PF05879_consen 437 ELKEPVESLLEN--PSPDMWDRIRKLFESATESAVSKFSDRLKGFGLSEEENEKALKKLRRK 496 (742)
T ss_pred HHhHHHHHHHhC--CChhhHHHHHHHHHHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHH
Confidence 344444444433 348999999999985433333333333333323356777777777744
No 161
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=20.78 E-value=59 Score=27.83 Aligned_cols=29 Identities=17% Similarity=0.138 Sum_probs=15.9
Q ss_pred ccccCCCCCcccc---cccCccccccCCCCcc
Q 036141 172 QCFSCKEYRHIVV---KCAKKFCNYCKKPGHI 200 (220)
Q Consensus 172 ~~~~~~~~g~~~~---~~~~~~C~~Cgk~GH~ 200 (220)
.|..|+....+-. ....-+||.||..|-.
T Consensus 36 ~CPfh~ek~pSf~v~~~k~~~~Cf~Cg~~Gd~ 67 (415)
T TIGR01391 36 LCPFHHEKTPSFSVSPEKQFYHCFGCGAGGDA 67 (415)
T ss_pred eCCCCCCCCCeEEEEcCCCcEEECCCCCCCCH
Confidence 3666655443211 1222379999988754
No 162
>PF08112 ATP-synt_E_2: ATP synthase epsilon subunit; InterPro: IPR012508 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. A-ATPases (or A1A0-ATPase) (3.6.3.14 from EC) are found exclusively in Archaea and display a close resemblance in structure and subunit composition with V-ATPases, although their function in both ATP synthesis and ATP hydrolysis is closer to that of F-ATPases []. A-ATPases are composed of two linked complexes: the A1 complex consisting of seven subunits contains the catalytic core that synthesizes/hydrolyses ATP, while the A0 complex consisting of at least two subunits forms the membrane-spanning pore []. The rotary motor in A-ATPases is composed of only two subunits, the stator subunit I and the rotor subunit C []. A-ATPases may have arisen as an adaptation to the different cellular needs and the more extreme environmental conditions faced by Archaeal species. The epsilon subunit is the smallest (7 kDa) of those found in the A1 complex. Unlike the A, B and C subunits, the epsilon subunit does not have a homologous counterpart in F- or V-ATPases []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0042626 ATPase activity, coupled to transmembrane movement of substances, 0015986 ATP synthesis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain
Probab=20.67 E-value=1.9e+02 Score=16.77 Aligned_cols=13 Identities=31% Similarity=0.398 Sum_probs=9.4
Q ss_pred HHhhccchHHHHH
Q 036141 100 FLMKLRPKYEAAR 112 (220)
Q Consensus 100 ~l~gLp~~~~~~~ 112 (220)
++..|+.+|..+.
T Consensus 27 il~~ln~EY~kiL 39 (56)
T PF08112_consen 27 ILSNLNMEYEKIL 39 (56)
T ss_pred HHHHHHHHHHHHH
Confidence 7777777777763
No 163
>cd07563 Peptidase_S41_IRBP Interphotoreceptor retinoid-binding protein; serine protease family S41. Interphotoreceptor retinoid-binding protein (IRBP) is a homolog of the S41 protease, C-terminal processing peptidase (CTPase) family. It is thought to facilitate the compartmentalization of the visual cycle that requires poorly soluble and potentially toxic retinoids to cross the aqueous subretinal space between the photoreceptors and the retinal pigment epithelium (RPE). IRBP is secreted by photoreceptors into the interphotoreceptor matrix (IPM) where it is rapidly turned over by a combination of RPE and photoreceptor endocytosis. It is the most abundant soluble protein component of the IPM, consisting of homologous modules, each repeat structure arising through the duplication (as in teleost IRBP) or quadruplication (in tetrapods) of an ancient gene, arisen in the early evolution of the vertebrate eye. IRBP has been shown to promote the release of all-trans retinol from photoreceptors
Probab=20.66 E-value=1.9e+02 Score=22.54 Aligned_cols=51 Identities=10% Similarity=-0.003 Sum_probs=33.6
Q ss_pred HHHHHHHHHHhccCCh--hHHhHHHHHHHHHhc-CCccHHHHHHHHHHHHHHHh
Q 036141 23 KDMWEYLKKVYNQDNT--AKRSHLEYEIARYSQ-GNLSIQNYFSGFQNLWAEYV 73 (220)
Q Consensus 23 ~~~w~~L~~~f~~~~~--~~~~~l~~~~~~~~q-~~~sv~~y~~~~~~l~~~L~ 73 (220)
..+|+.|++.|..... ..-..++.++..... ...+-.++...|..+...|.
T Consensus 3 ~~~~~~~~~~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~l~ 56 (250)
T cd07563 3 EALAKLLEENYAFPEAKGIDWDALAARLRAQVYLDITSPEELAAVLTADLQELG 56 (250)
T ss_pred HHHHHHHHHhCCChHHcccHHHHHHHHHhccccccCCCHHHHHHHHHHhhhccC
Confidence 5688888888873221 133444555555555 66788888888888877764
No 164
>KOG2607 consensus CDK5 activator-binding protein [Signal transduction mechanisms]
Probab=20.10 E-value=2.6e+02 Score=24.07 Aligned_cols=80 Identities=18% Similarity=0.211 Sum_probs=42.9
Q ss_pred HHHHHHHHHHHhccCC--hhHHh------------HHHHHHHHHhc----------C-CccHHHHHHHHHHHHHHHhhcc
Q 036141 22 AKDMWEYLKKVYNQDN--TAKRS------------HLEYEIARYSQ----------G-NLSIQNYFSGFQNLWAEYVDMI 76 (220)
Q Consensus 22 a~~~w~~L~~~f~~~~--~~~~~------------~l~~~~~~~~q----------~-~~sv~~y~~~~~~l~~~L~~~~ 76 (220)
....|..+...|++.. .+... .|+.++..+.| + +.+..+-...|...+.+|. +-
T Consensus 91 rmkdwqeivr~yEkd~~YlaEaAQIlvrnvnYEIP~LkKQiaK~qQq~tE~~RKe~d~~k~aa~~r~qfe~~c~qlg-lk 169 (505)
T KOG2607|consen 91 RMKDWQEIVRAYEKDHIYLAEAAQILVRNVNYEIPYLKKQIAKVQQQMTELDRKEADIKKSAALSRTQFEDACRQLG-LK 169 (505)
T ss_pred cccCHHHHHHHHhcCceeHHHHHHHHHHhccccccHHHHHHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHhC-Cc
Confidence 4567888888888533 22222 23333333322 2 4555556666666666665 43
Q ss_pred cccCCcccHHHHHHHHHHHHHHHHHhhccchHHHHHHhh
Q 036141 77 YVQVPIESLADVQEVHEQSKRDQFLMKLRPKYEAARSNL 115 (220)
Q Consensus 77 ~~~~~~~~~~~~~~~~~~~~~~~~l~gLp~~~~~~~~~l 115 (220)
|..+..+.+ .++.+||+.|..+....
T Consensus 170 G~nvr~ElL-------------elasdLPs~fyei~~v~ 195 (505)
T KOG2607|consen 170 GNNVRRELL-------------ELASDLPSTFYEILEVI 195 (505)
T ss_pred cchHHHHHH-------------HHHhcCcHHHHHHHHHH
Confidence 544433322 26778887766554433
Done!